Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic.

The global prevalence of the XBB lineage presents a formidable challenge posed by the recombinant SARS-CoV-2 virus. The understanding of SARS-CoV-2's recombination preference assumes utmost significance in predicting future recombinant variants and adequately preparing for subsequent pandemics. Thus, an urgent need arises to establish a comprehensive landscape concerning SARS-CoV-2 recombinants worldwide and elucidate their evolutionary mechanisms. However, the initial step, involving the detection of potential recombinants from a vast pool of over 10 million sequences, presents a significant obstacle. In this study, we present CovRecomb, a lightweight methodology specifically designed to effectively identify and dissect interlineage SARS-CoV-2 recombinants. Leveraging CovRecomb, we successfully detected 135,567 putative recombinants across the entirety of 14.5 million accessed SARS-CoV-2 genomes. These putative recombinants could be classified into 1451 distinct recombination events, of which 206 demonstrated transmission spanning multiple countries, continents, or globally. Hotspot regions were identified in six specific areas, with prominence observed in the latter halves of the N-terminal domain and receptor-binding domain within the spike (S) gene. Epidemiological investigations revealed extensive recombination events occurring among different SARS-CoV-2 (sub)lineages, independent of lineage prevalence frequencies.

Comparative analysis of chromosome-level genomes provides insights into chromosomal evolution in Chiroptera.

Chiroptera (bats) presents a fascinating model due to its remarkable variation in chromosome numbers, which range from 14 to 62. This astonishing diversity makes bats an excellent subject for studying chromosome evolution. The black-bearded tomb bat (Taphozous melanopogon) occupies a pivotal phylogenetic position within Chiroptera, emphasizing its crucial role in the systematic examination of bat chromosome evolution. In this study, we present the first chromosome-level genome of T. melanopogon within the family Emballonuridae. Together with previously published genomes, we construct a strongly supported phylogenetic tree of bats, which supports that Emballonuridae forms a basal group within Yangochiroptera. Furthermore, we reconstruct ancestral karyotypes at key nodes along the bat phylogeny and conduct a synteny analysis among the genomes of 12 bat species. Our findings identified evolutionary breakpoint regions (EBRs) that are of particular interest. Notably, some bat genomes exhibit an enrichment of genes related to host defense against microbial pathogens within EBRs. Remarkably, one species possesses multiple copies of some ß-defensin genes, while six other species have experienced the loss of some ß-defensin genes due to EBRs. Furthermore, some olfactory receptor genes are located in EBRs of 12 species, 4 of which have a significant enrichment in sensory perception of smell. Together, our comparative genomic analysis underscores the potential link between chromosome rearrangements and the adaptation of bats to defend against microbial pathogens.

Overcoming the pitfalls of categorizing continuous variables in ecology, evolution and behaviour.

Many variables in biological research-from body size to life-history timing to environmental characteristics-are measured continuously (e.g. body mass in kilograms) but analysed as categories (e.g. large versus small), which can lower statistical power and change interpretation. We conducted a mini-review of 72 recent publications in six popular ecology, evolution and behaviour journals to quantify the prevalence of categorization. We then summarized commonly categorized metrics and simulated a dataset to demonstrate the drawbacks of categorization using common variables and realistic examples. We show that categorizing continuous variables is common (31% of publications reviewed). We also underscore that predictor variables can and should be collected and analysed continuously. Finally, we provide recommendations on how to keep variables continuous throughout the entire scientific process. Together, these pieces comprise an actionable guide to increasing statistical power and facilitating large synthesis studies by simply leaving continuous variables alone. Overcoming the pitfalls of categorizing continuous variables will allow ecologists, ethologists and evolutionary biologists to continue making trustworthy conclusions about natural processes, along with predictions about their responses to climate change and other environmental contexts.

Adult Philadelphia-Positive Acute Lymphoblastic Leukemia: A Single-Institution Experience in Limited-Resource Setting.

L. K. RajeevBackground Adult Philadelphia-positive (Ph + ) acute lymphoblastic leukemia (ALL) is a distinct entity with poor prognosis. Treatment with tyrosine kinase inhibitors improved responses but still with poor outcomes. We evaluated treatment outcomes in these patients treated in limited-resource settings in the absence of availability of allogeneic stem cell transplantation (ASCT). Materials and Methods We studied case record files of the adult patients diagnosed with Ph+ ALL. Results A total of 18 patients were evaluated retrospectively. The median age of presentation was 28 years. Male-to-female ratio was 1:1. Patients presented with fever and fatigue. Six patients (33.33%) presented with cervical lymphadenopathy. Clinical splenomegaly was present in 16 (88.88%) patients on palpation, whereas on ultrasonographic evaluation, all 18 patients had splenomegaly. The median size of the spleen was 15 cm. Hepatomegaly was seen in 5 (27%) patients. All 18 patients had anemia at the time of presentation. Leukocytosis was seen in 17 (94.44%) patients, whereas 1 (5.56%) patient presented with low total leukocyte count. The median platelet count at the time of presentation was 30,000/mm. 3 On peripheral smear, median number of blast cells was 55%, and on bone marrow aspiration samples, median blast percentage seen was 70%. Conventional cytogenetics was done in all the patients on bone marrow aspiration samples. Ten patients (55.55%) had t(9;22) - Ph chromosome. One patient (5.56%) on cytogenetics showed double Ph chromosome. The median value of breakpoint cluster region-ABL1 transcript in IS% was 13%. Seventeen (94.44%) received ALL protocol (BFM95) along with tyrosine kinase inhibitor (imatinib). One (5.56%) patient refused aggressive cytotoxic chemotherapy. No patient underwent ASCT. The median duration of follow-up was 7.5 months, ranging from 3 to 16 months. Median overall survival (OS) was 7.5 months and 2-year OS was 33.33%. Conclusion Poor prognosis of this disease, especially in the absence of ASCT, remains a major challenge in the treatment.

Comprehensive analysis of chromosomal breakpoints and candidate genes associated with male infertility: insights from cytogenetic studies and expression analyses.

The study aimed to investigate prevalent chromosomal breakpoints identified in balanced structural chromosomal anomalies and to pinpoint potential candidate genes linked with male infertility. This was acchieved through a comprehensive approach combining RNA-seq and microarray data analysis, enabling precise identification of candidate genes. The Cytogenetics data from 2,500 infertile males referred to Royan Research Institute between 2009 and 2022 were analyzed, with 391 cases meeting the inclusion criteria of balanced chromosomal rearrangement. Of these, 193 cases exhibited normal variations and were excluded from the analysis. By examining the breakpoints, potential candidate genes were suggested. Among the remaining 198 cases, reciprocal translocations were the most frequent anomaly (129 cases), followed by Robertsonian translocations (43 cases), inversions (34 cases), and insertions (3 cases).Some patients had more than one chromosomal abnormality. Chromosomal anomalies were most frequently observed in chromosomes 13 (21.1%), 14 (20.1%), and 1 (16.3%) with 13q12, 14q12, and 1p36.3 being the most prevalent breakpoints, respectively. Chromosome 1 contributed the most to reciprocal translocations (20.2%) and inversions (17.6%), while chromosome 14 was the most involved in the Robertsonian translocations (82.2%). The findings suggested that breakpoints at 1p36.3 and 14q12 might be associated with pregestational infertility, whereas breakpoints at 13q12 could be linked to both gestational and pregestational infertility. Several candidate genes located on common breakpoints were proposed as potentially involved in male infertility. Bioinformatics analyses utilizing three databases were conducted to examine the expression patterns of 78 candidate genes implicated in various causes of infertility. In azoospermic individuals, significant differential expression was observed in 19 genes: 15 were downregulated (TSSK2, SPINK2, TSSK4, CDY1, CFAP70, BPY2, BTG4, FKBP6, PPP2R1B, SPECC1L, CENPJ, SKA3, FGF9, NODAL, CLOCK), while four genes were upregulated ( HSPB1, MIF, PRF1, ENTPD6). In the case of Asthenozoospermia, seven genes showed significant upregulation (PRF1, DDX21, KIT, SRD5A3, MTCH1, DDX50, NODAL). Though RNA-seq data for Teratozoospermia were unavailable, microarray data revealed differential expression insix genes: three downregulated (BUB1, KLK4, PIWIL2) and three upregulated (AURKC, NPM2, RANBP2). These findings enhance our understanding of the molecular basis of male infertility and could provide valuable insights for future diagnostic and therapeutic strategies.

DNA methylation dysregulation patterns in the 1p36 region instability.

In the monosomy 1p36 deletion syndrome, the role of DNA methylation in the genomic stability of the 1p36 region remains elusive. We hypothesize that changes in the methylation pattern at the 1p36 breakpoint hotspot region influenced the chromosomal breakage leading to terminal deletions. From the monosomy 1p36 material collection, four cases with 4.0 to 5.5 Mb terminal deletions and their parents were investigated. DNA samples were assessed by targeted bisulfite sequencing (NimbleGen SeqCap Epi) to examine DNA methylation status in the 1p36 hotspot region at single-base resolution as compared to the chromosomal hotspot regions, 9p22, 18q21.1, and 22q11.2. Additionally, in in silico assessment, the mean GC content of various classes of repeats in the genome and especially in the breakpoint regions was evaluated. A complex landscape of DNA methylation in the 1p36 breakpoint hotspot region was found. Changes in DNA methylation level in the vicinity of the breakpoint in the child's DNA when compared to parents' and control DNA were observed, with a shift from 15.1 to 70.8% spanning the breakpoint region. In the main classes of evaluated repeats, higher mean GC contents in the 1p36 breakpoint region (47.06%), 22q11.2 (48.47%), and 18q21.1 (44.21%) were found, compared to the rest of the genome (40.78%). The 9p22 region showed a lower GC content (39.42%) compared to the rest of the genome. Both dysregulation of DNA methylation and high GC content were found to be specific for the 1p36 breakpoint hotspot region suggesting that methylation abnormalities could contribute to aberrations at 1p36.

Clinical validation and application of targeted long-range polymerase chain reaction and long-read sequencing-based analysis for hemophilia: experience from a hemophilia treatment center in China.

BACKGROUND: Targeted long-read sequencing (LRS) is expected to comprehensively analyze diverse complex variants in hemophilia A (HA) and hemophilia B (HB) caused by the F8 and F9 genes, respectively. However, its clinical applicability still requires extensive validation. OBJECTIVES: To evaluate the clinical applicability of targeted LRS-based analysis compared with routine polymerase chain reaction (PCR)-based methods. METHODS: Gene variants of retrieved subjects were retrospectively and prospectively analyzed. Whole-genome sequencing was performed to further analyze undiagnosed cases. Breakpoints of novel genomic rearrangements were mapped and validated using long-distance PCR and long-range PCR combined with sequencing. RESULTS: In total, 122 subjects were retrieved. In retrospective analysis of the 90 HA cases, HA-LRS assay showed consistent results in 84 cases compared with routine methods and characterized 6 large deletions with their exact breakpoints confirmed by further validation in 6 cases (routine methods only presented failure in amplifying the involved exons). In prospective analysis of the 21 HA subjects, 20 variants of F8 were identified in 20 cases. For the remaining HA patient, no duplication/deletion or single-nucleotide variant (SNV)/insertion and deletion (InDel) was found, but a potential recombination involving exons 14 and 21 of F8 was observed by LRS. Whole-genome sequencing analysis and further verification defined a 30 478 base pairs (bp) tandem repeat involving exons 14 to 21 of F8. Among the 11 HB patients, HB-LRS analysis detected 11 SNVs/InDels in F9, consistent with routine methods. CONCLUSION: Targeted LRS-based analysis was efficient and comprehensive in identifying SNVs/InDels and genomic rearrangements of hemophilia genes, especially when we first expanded the panel to include F9. However, further investigation for complex gross rearrangement is still essential.

ENOVAT: the European Network for Optimization of Veterinary Antimicrobial Treatment.

The global antimicrobial resistance crisis has been the driver of several international strategies on antimicrobial stewardship. For their implementation at the field level, the veterinary sector encounters several specific challenges and in particular: (i) a shortage of experts in key disciplines related to antimicrobial stewardship, (ii) a lack of evidence-based antimicrobial treatment guidelines, and (iii) inferior diagnostic tests available compared to human medicine. The present white paper describes how the COST Action ENOVAT (the European Network for Optimization of Veterinary Antimicrobial Treatment, CA18217), comprising 332 persons from 51 countries, worked towards solutions to these challenges. Initially, surveys were conducted to explore the present state in Europe in terms of existing antimicrobial use guidelines and microbiology practices performed. Concurrently, various research activities were launched to optimize diagnostics, including development of epidemiological cut-offs, clinical breakpoints and matrix-assisted laser desorption ionization time of flight mass spectrometry interpretive criteria. Also, guidelines drafting groups working towards evidence-based antimicrobial treatment guidelines for six conditions in food-producing and companion animals were established. The processes and outcomes, also in terms of capacity building, are summarized in this white paper where emphasis is placed on sustainability of the activities. Although several ENOVAT initiatives and spin-off projects will continue beyond the Action, we recommend that a new European veterinary research agenda is launched focusing on research and funding leading to long-term impacts on veterinary antimicrobial use.

Antimicrobial resistance is an urgent global public health threat that is amplified by over- and misuse of antimicrobials. As a result of antimicrobial resistance, antibiotics and other antimicrobial medicines become ineffective and infections become difficult or impossible to treat. This goes for human infections, but also for infections in animals. In a recently finished European project called ENOVAT we tried to tackle the problem of antimicrobial resistance in animals. We focused on two topics. First we optimized and harmonized diagnostics of bacterial infections in the laboratory, and second we developed evidence-based treatment guidelines to support veterinary practitioners on how and when to use antibiotics in the best way. Improved diagnostics and new treatment guidelines can help veterinary practitioners to a more sensible antibiotic choice and with that less over- and misuse of antimicrobials. This article summarizes the process and progress of the work done in the ENOVAT project. Emphasis is also put on how the project benefitted from a unique consortium encompassing 332 professionals with diverse backgrounds, from 51 countries.

Profiles of muscle-specific oxygenation responses and thresholds during graded cycling incremental test.

Compared to the determination of exercise thresholds based on systemic changes in blood lactate concentrations or gas exchange data, the determination of breakpoints based on muscle oxygen saturation offers a valid alternative to provide specific information on muscle-derived thresholds. Our study explored the profiles and timing of the second muscle oxygenation threshold (MOT2) in different muscles. Twenty-six cyclists and triathletes (15 male: age = 23 ± 7 years, height = 178 ± 5 cm, body mass = 70.2 ± 5.3 kg; 11 female: age = 22 ± 4 years, height = 164 ± 4 cm, body mass = 58.3 ± 8.1 kg) performed a graded exercise test (GXT), on a cycle ergometer. Power output, blood lactate concentration, heart rate, rating of perceived exertion, skinfolds and muscle oxygen saturation were registered in five muscles (vastus lateralis, biceps femoris, gastrocnemius medialis, tibialis anterior and triceps brachii) and percentage at which MOT2 occurred for each muscle was determinated using the Exponential Dmax. The results of Statistical Parametric Mapping and ANOVA showed that, although muscle oxygenation displayed different profiles in each muscle during a GXT, MOT2 occurred at a similar percentage of the GXT in each muscle (77% biceps femoris, 75% tibalis anterior, 76% gastrocnemius medialis and 72% vastus lateralis) and it was similar that systemic threshold (73% of the GXT). In conclusion, this study showed different profiles of muscle oxygen saturation in different muscles, but without notable differences in the timing for MOT2 and concordance with systemic threshold. Finally, we suggest the analysis of the whole signal and not to simplify it to a breakpoint.

Ikaros Deletions among Bulgarian Patients with Acute Lymphoblastic Leukemia/Lymphoma.

The Ikaros zinc finger factor 1 is a transcription factor with a well-known role in B- and T-cell development. The deletions of IKZF1 have an established significance in acute lymphoblastic leukemia, while reports on its prevalence and prognostic significance among ALL subtypes and regions vary. Breakpoint-specific qPCR is a practical method for testing of the most frequent types of IKZF1 deletions, considering there is clustering of the deletion events. The most commonly reported deletions are Δ4-7, Δ4-8, Δ2-7, and Δ2-8, with deletion Δ4-7 being the most common one. We retrospectively administered a breakpoint-specific qPCR design for screening for the most frequent types of IKZF1 deletions to 78 ALL patients that were diagnosed and treated between 2010 and 2022. We observed the products through gel electrophoresis, and we conducted descriptive statistics, EFS, and OS analyses. Our study found 19 patients with IKZF1 deletions, with two subjects manifesting more than one deletion. The prevalence in the different subgroups was as follows: Ph/+/ B-ALL 46%, Ph/-/ B-ALL 30%, T-ALL/LBL 4%. There was a statistically significant difference in EFS of 39 vs. 0% in favor of patients without deletions (p = 0.000), which translated to a difference in OS of 49 vs. 0% (p = 0.001). This difference was preserved in the subgroup of Ph/-/ B-ALL, while there was no significant difference in the Ph/+/ B-ALL. The most frequently observed type of deletion (15 out of 19) was the Δ4-7. There is a strong negative prognostic impact of the IKZF1 deletions at diagnosis in the observed population. IKZF1 deletion testing through breakpoint-specific qPCR is a practical approach in diagnostic testing for this risk factor. IKZF1 deletions may warrant treatment decisions and intensified treatment strategies to overcome the negative prognostic impact.

In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo.

Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating the electrolytes' balance in kidneys and other organs. In order to define the chloride voltage-gated channel (CLCN) gene family in buffalo, this study used in silico analyses to examine physicochemical properties, evolutionary patterns, and genome-wide identification. We identified eight CLCN genes in buffalo. The ProtParam tool analysis identified a number of important physicochemical properties of these proteins, including hydrophilicity, thermostability, in vitro instability, and basic nature. Based on their evolutionary relationships, a phylogenetic analysis divided the eight discovered genes into three subfamilies. Furthermore, a gene structure analysis, motif patterns, and conserved domains using TBtool demonstrated the significant conservation of this gene family among selected species over the course of evolution. A comparative amino acid analysis using ClustalW revealed similarities and differences between buffalo and cattle CLCN proteins. Three duplicated gene pairs were identified, all of which were segmental duplications except for CLCN4-CLCN5, which was a tandem duplication in buffalo. For each gene pair, the Ka/Ks test ratio findings showed that none of the ratios was more than one, indicating that these proteins were likely subject to positive selection. A synteny analysis confirmed a conserved pattern of genomic blocks between buffalo and cattle. Transcriptional control in cells relies on the binding of transcription factors to specific sites in the genome. The number of transcription factor binding sites (TFBSs) was higher in cattle compared to buffalo. Five main recombination breakpoints were identified at various places in the recombination analysis. The outcomes of our study provide new knowledge about the CLCN gene family in buffalo and open the door for further research on candidate genes in vertebrates through genome-wide studies.

Incentive motivation for palatable food blocked by intra-accumbens melanin-concentrating hormone (MCH) receptor-1 antagonist in female rats.

Melanin-concentrating hormone (MCH) activity in the nucleus accumbens (Acb) has been shown to influence feeding behavior, yet this has not been characterized in terms of homeostatic vs. hedonic feeding processes. Hedonic feeding, driven by palatability rather than energy deficit, can be modeled through intra-Acb administration of the selective µ-opioid receptor agonist d-Ala2, NMe-Phe4, Glyol5-enkephalin (DAMGO), which preferentially increases consumption and incentive motivation to obtain preferred palatable food. Pharmacological activation of MCH 1 receptors (MCHR1) within Acb has been shown to promote general feeding of chow in males, but not females. However, the effects of MCH on the incentive motivation to obtain preferred palatable food have not been explored. Here, we investigated the role of MCHR1 within the Acb in DAMGO-induced incentive motivation to obtain a sucrose pellet reward. Female Sprague Dawley rats were trained and tested for operant responding under a progressive ratio (PR) breakpoint in response to concurrent intra-Acb administration of DAMGO (0 µg and 0.025 µg/.5 µl/side) immediately following intra-Acb administration of the MCHR1 antagonist (N-(3-{1-[4-(3,4-difluoro-phenoxy)-benzyl]-piperdin-4-yl}-4-methyl-phenyl)-isobutyramide (SNAP-94847; 0 µg, 1.5 µg, and 15 µg/.5 µl/side), in a counterbalanced fashion. As expected, DAMGO significantly increased PR breakpoint and overall active lever presses. SNAP-94847 did not influence PR breakpoint by itself, compared to vehicle; however, both 1.5 and 15 µg doses of SNAP-94847 significantly blocked the increased PR breakpoint produced by intra-Acb DAMGO. The results of the study demonstrate that Acb MCHR1 may play a specific role in the hedonically-driven motivation for palatable food in females.

Antibacterial action of penicillin against Mycobacterium avium complex.

INTRODUCTION: ß-lactam antibiotics are promising treatments for Mycobacterium avium complex (MAC) lung disease. We hypothesized that benzylpenicillin has efficacy against MAC. METHODS: Benzylpenicillin lung concentration-time profiles of seven doses in three dosing schedules were administered for 28 days using the hollow fiber system model of intracellular MAC (HFS-MAC). Data were analyzed using the inhibitory sigmoid maximal effect (Emax) model for each sampling day, while two ordinary differential equations (ODEs) were used for the wild-type and penicillin-resistant mutants. RESULTS: Benzylpenicillin killed >2.1 log10 colony-forming unit (CFU)/mL below Day 0, better than azithromycin, ethambutol, and rifabutin. Efficacy was terminated by acquired resistance. Sigmoid Emax parameter estimates significantly differed between sampling days and were a poor fit. However, ODE model parameter estimates vs. exposure were a better fit. The exposure mediating Emax was 84.6% (95% CI 76.91-82.98) of time concentration exceeded the minimum inhibitory concentration (MIC). In Monte Carlo experiments, 24 million international units of benzylpenicillin continuous infusion achieved the target exposure in lungs of >90% of 10,000 subjects until an MIC of 64 mg/L, designated the susceptibility breakpoint. CONCLUSIONS: Benzylpenicillin demonstrated a better bactericidal effect against MAC than guideline-recommended drugs before the development of resistance. Its role in combination therapy with other drugs with better efficacy than guideline-recommended drugs should be explored.

INTRODUCTION: Les ß-lactamines représentent des options thérapeutiques prometteuses pour le traitement de la maladie pulmonaire à complexe Mycobacterium avium (MAC). Notre hypothèse suggère que la benzylpénicilline pourrait être efficace contre cette maladie pulmonaire causée par M. avium. MÉTHODES: Les concentrations pulmonaires de benzylpénicilline ont été mesurées à différents moments après l'administration de sept doses selon trois schémas différents pendant 28 jours dans le modèle de MAC intracellulaire du système de fibres creuses (HFS-MAC). Les données ont été analysées en utilisant un modèle sigmoïde inhibiteur à effet maximal (Emax) pour chaque jour d'échantillonnage, et deux équations différentielles ordinaires (ODE) ont été appliquées pour les souches sauvages et les mutants résistants à la pénicilline. RÉSULTATS: La benzylpénicilline a provoqué une réduction de >2,1 log10 CFU/mL en dessous du jour 0, surpassant ainsi l'azithromycine, l'éthambutol et la rifabutine. Cependant, son efficacité a été compromise par l'émergence d'une résistance. Les estimations des paramètres de l'Emax sigmoïde ont montré des différences significatives entre les jours d'échantillonnage et étaient mal ajustées. En revanche, les estimations des paramètres du modèle ODE en fonction de l'exposition étaient plus précises. L'exposition médiane de l'Emax était de 84,6% (IC à 95% 76,91­82,98) du temps où la concentration dépassait la concentration minimale inhibitrice (MIC, pour l'anglais « minimum inhibitory concentration ¼). Dans les simulations de Monte Carlo, une perfusion continue de 24 millions d'unités internationales de benzylpénicilline a permis d'atteindre l'exposition cible dans les poumons de plus de 90% des 10 000 sujets, jusqu'à ce qu'une MIC de 64 mg/L soit atteinte, indiquant ainsi le point de rupture de la sensibilité. CONCLUSIONS: La benzylpénicilline a montré une efficacité bactéricide supérieure contre le MAC par rapport aux médicaments recommandés par les lignes directrices avant l'émergence de la résistance. Il convient d'explorer son utilisation dans une thérapie combinée avec des médicaments plus performants que ceux recommandés par les lignes directrices.

Self-supported iron-doped cobalt-copper oxide heterostructures for efficient electrocatalytic denitrification.

The electrocatalytic reduction of nitrate ions (NO3-) to nitrogen gas (N2) has emerged as an effective approach for mitigating nitrate pollution in water bodies. However, the development of efficient and highly selective cathode materials remains challenging. Conventional copper-based catalysts often exhibit low selectivity because they strongly adsorb oxygen. In this study, a straightforward solvothermal and pyrolysis method was used to grow iron-doped cobalt-copper oxide heterogeneous structures on copper foam surfaces (Fe-CoO/CuO@CF). Then, the effects of the applied potential, initial NO3- concentration, Cl- concentration, electrolyte pH, and different catalysts on the catalyst performance were investigated. Compared with recently reported congeners, Fe-CoO/CuO@CF is less expensive and exhibits outstanding activity for NO3- reduction. Meanwhile, under a cathode potential of - 1.31 V vs. Ag/AgCl, Fe-CoO/CuO@CF degrades 98.6 % of NO3- in 200 min. In addition, when employing a method inspired by NH4+ removal by breakpoint chlorination, N2 selectivity over Fe-CoO/CuO@CF was raised from 10 % without Cl- to 99.7 % when supplemented with Cl-. The catalyst demonstrated excellent cyclic stability, maintaining a high electrocatalytic activity for the conversion of NO3- to N2 gas over eleven cycles. Moreover, Fe-CoO/CuO@CF enabled 63.7 % removal of NO3- from wastewater (50 mg/L NO3--N) prepared from natural water, with 100 % conversion to N2. Computational studies showed that iron doping decreased the free energy change of the intermediate of NO3- reduction reaction. This study provides an effective strategy for the electrochemical reduction of nitrate to nitrogen gas and offers good prospects for addressing nitrate pollution.

Glass syndrome derived from chromosomal breakage downstream region of SATB2.

BACKGROUND: Glass syndrome, derived from chromosomal 2q33.1 microdeletions, manifests with intellectual disability, microcephaly, epilepsy, and distinctive features, including micrognathia, down-slanting palpebral fissures, cleft palate, and crowded teeth. Recently, SATB2 located within the deletion region, was identified as the causative gene responsible for Glass syndrome. Numerous disease-causing variants within the SATB2 coding region have been reported. OBJECTIVE: Given the presentation of intellectual disability and multiple congenital anomalies in a patient with a de novo reciprocal translocation between chromosomes 1 and 2, disruption of the causative gene(s) was suspected. This study sought to identify the causative gene in the patient. METHODS: Long-read whole-genome sequencing was performed, and the expression level of the candidate gene was analyzed. RESULTS: The detection of breakpoints was successful. While the breakpoint on chromosome 1 disrupted RNF220, it was not deemed to be a genetic cause. Conversely, SATB2 is located in the approximately 100-kb telomeric region of the breakpoint on chromosome 2. The patient's clinical features resembled those of previously reported cases of Glass syndrome, despite the lack of confirmed reduced SATB2 expression. CONCLUSION: The patient was diagnosed with Glass syndrome due to the similarity in clinical features. This led us to hypothesize that disruption in the downstream region of SATB2 could result in Glass syndrome. The microhomologies identified in the breakpoint junctions indicate a potential molecular mechanism involving microhomology-mediated break-induced repair mechanism or template switching.

A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira.

Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift-giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing data set to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the 6 chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.

Multicenter study on clinical outcomes and poor prognostic factors in patients with Klebsiella pneumoniae bacteremia receiving cefoperazone/sulbactam treatment.

BACKGROUND: Infections caused by Klebsiella pneumoniae are common and result in high mortality rates. In vitro studies demonstrated the potency of cefoperazone/sulbactam (CPZ/SUL) against Klebsiella pneumoniae. However, the clinical efficacy of CPZ/SUL for the treatment of K. pneumoniae bacteremia has not been studied. OBJECTIVES: This study aimed to associate the clinical outcomes of patients with bacteremia with the minimal inhibitory concentrations (MICs) of CPZ/SUL against the causative K. pneumoniae isolates. METHODS: This multicenter, retrospective study was conducted in Taiwan between July 2017 and April 2021. Patients with K. pneumoniae bacteremia treated with CPZ/SUL were enrolled in this study. CPZ/SUL MICs were determined using the agar dilution method. Data on the patients' clinical outcomes and characteristics were collected and analyzed. RESULTS: In total, 201 patients were enrolled. Among the causative K. pneumoniae isolates, 180 (89.5%) were susceptible to CPZ/SUL. Most patients (n = 156, 77.6%) had favorable outcomes. The 30-day mortality rate was 11.9% (n = 24). Multivariate risk analyses showed that higher APACHE II score (Odds Ratio [OR], 1.14; Confidence Interval [CI], 1.07-1.21; p < 0.001), metastatic tumors (OR, 5.76; CI, 2.31-14.40; p < 0.001), and causative K. pneumoniae CPZ/SUL MICs > 16 µg/ml (OR, 4.30; CI, 1.50-12.27; p = 0.006) were independently associated with unfavorable outcomes. CONCLUSION: Patients with K. pneumoniae bacteremia treated with CPZ/SUL at a ratio 1:1 had favorable outcomes when the CPZ/SUL MICs were ≤ 16 µg/ml. Patients with higher APACHE II scores and metastatic tumors had unfavorable outcomes.

A new objective method for determining exercise gas exchange thresholds by respiratory frequency in middle-aged men.

PURPOSE: To evaluate the agreement between the two Gas Exchange Thresholds (GETs = GET1 and GET2), identified by the conventional V-Slope method, and two Respiratory Frequency Thresholds (fRTs = fRT1 and fRT2) obtained from a novel, low-cost, and simple method of breakpoint determination. METHODS: Fifty middle-aged males (age: 50-58 years; V ˙ o2peak: 37.5 ± 8.6 mL·Kg-1·min-1), either healthy or with chronic illnesses, underwent an incremental cycle exercise test to determine maximal oxygen uptake ( V ˙ o2max/ V ˙ o2peak), GETs and fRTs. RESULTS: There were no statistical differences [P > 0.05; ES: 0.17 to 0.32, small] between absolute and relative (56-60% V ˙ o2peak) oxygen uptake ( V ˙ o2) values at GET1 with those obtained at fRT1, nor between V ˙ o2 values at GET2 with those at fRT2 (76-78% V ˙ o2peak). Heart rate (HR) at fRT1, and V ˙ o2 and HR at fRT2 showed very large correlations (r = 0.75-0.82; P < 0.001) and acceptable precision (SEE < 7-9%) in determination of their corresponding values at GET1 and GET2. The precision in the estimation of V ˙ o2 at GET1 from fRT1 was moderate (SEE = 15%), while those of power output at GET1 (SEE = 23%) and GET2 (SEE = 12%) from their corresponding fRTs values were very poor to moderate. CONCLUSION: HR at fRT1 and V ˙ o2 and HR at fRT2, determined using a new objective and portable approach, may potentially serve as viable predictors of their respective GETs. This method may offer a simplified, cost-effective, and field-based approach for determining exercise threshold intensities during graded exercise.

Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints.

Phylogenetic methods are widely used to reconstruct the evolutionary relationships among species and individuals. However, recombination can obscure ancestral relationships as individuals may inherit different regions of their genome from different ancestors. It is, therefore, often necessary to detect recombination events, locate recombination breakpoints, and select recombination-free alignments prior to reconstructing phylogenetic trees. While many earlier studies have examined the power of different methods to detect recombination, very few have examined the ability of these methods to accurately locate recombination breakpoints. In this study, we simulated genome sequences based on ancestral recombination graphs and explored the accuracy of three popular recombination detection methods: MaxChi, 3SEQ, and Genetic Algorithm Recombination Detection. The accuracy of inferred breakpoint locations was evaluated along with the key factors contributing to variation in accuracy across datasets. While many different genomic features contribute to the variation in performance across methods, the number of informative sites consistent with the pattern of inheritance between parent and recombinant child sequences always has the greatest contribution to accuracy. While partitioning sequence alignments based on identified recombination breakpoints can greatly decrease phylogenetic error, the quality of phylogenetic reconstructions depends very little on how breakpoints are chosen to partition the alignment. Our work sheds light on how different features of recombinant genomes affect the performance of recombination detection methods and suggests best practices for reconstructing phylogenies based on recombination-free alignments.

A machine learning framework for spatio-temporal vulnerability mapping of groundwaters to nitrate in a data scarce region in Lenjanat Plain, Iran.

The temporal aspect of groundwater vulnerability to contaminants such as nitrate is often overlooked, assuming vulnerability has a static nature. This study bridges this gap by employing machine learning with Detecting Breakpoints and Estimating Segments in Trend (DBEST) algorithm to reveal the underlying relationship between nitrate, water table, vegetation cover, and precipitation time series, that are related to agricultural activities and groundwater demand in a semi-arid region. The contamination probability of Lenjanat Plain has been mapped by comparing random forest (RF), support vector machine (SVM), and K-nearest-neighbors (KNN) models, fed with 32 input variables (dem-derived factors, physiography, distance and density maps, time series data). Also, imbalanced learning and feature selection techniques were investigated as supplementary methods, adding up to four scenarios. Results showed that the RF model, integrated with forward sequential feature selection (SFS) and SMOTE-Tomek resampling method, outperformed the other models (F1-score: 0.94, MCC: 0.83). The SFS techniques outperformed other feature selection methods in enhancing the accuracy of the models with the cost of computational expenses, and the cost-sensitive function proved more efficient in tackling imbalanced data issues than the other investigated methods. The DBEST method identified significant breakpoints within each time series dataset, revealing a clear association between agricultural practices along the Zayandehrood River and substantial nitrate contamination within the Lenjanat region. Additionally, the groundwater vulnerability maps created using the candid RF model and an ensemble of the best RF, SVM, and KNN models predicted mid to high levels of vulnerability in the central parts and the downhills in the southwest.