Metagenome comparison (MC): A new framework for detecting unique/enriched OMUs (operational metagenomic units) derived from whole-genome sequencing reads.

BACKGROUND: Current methods for comparing metagenomes, derived from whole-genome sequencing reads, include top-down metrics or parametric models such as metagenome-diversity, and bottom-up, non-parametric, model-free machine learning approaches like Naïve Bayes for k-mer-profiling. However, both types are limited in their ability to effectively and comprehensively identify and catalogue unique or enriched metagenomic genes, a critical task in comparative metagenomics. This challenge is significant and complex due to its NP-hard nature, which means computational time grows exponentially, or even faster, with the problem size, rendering it impractical for even the fastest supercomputers without heuristic approximation algorithms. METHOD: In this study, we introduce a new framework, MC (Metagenome-Comparison), designed to exhaustively detect and catalogue unique or enriched metagenomic genes (MGs) and their derivatives, including metagenome functional gene clusters (MFGC), or more generally, the operational metagenomic unit (OMU) that can be considered the counterpart of the OTU (operational taxonomic unit) from amplicon sequencing reads. The MC is essentially a heuristic search algorithm guided by pairs of new metrics (termed MG-specificity or OMU-specificity, MG-specificity diversity or OMU-specificity diversity). It is further constrained by statistical significance (P-value) implemented as a pair of statistical tests. RESULTS: We evaluated the MC using large metagenomic datasets related to obesity, diabetes, and IBD, and found that the proportions of unique and enriched metagenomic genes ranged from 0.001% to 0.08 % and 0.08%-0.82 % respectively, and less than 10 % for the MFGC. CONCLUSION: The MC provides a robust method for comparing metagenomes at various scales, from baseline MGs to various function/pathway clusters of metagenomes, collectively termed OMUs.

Emergency department utilization among adults with epilepsy: A multi-state cross-sectional analysis, 2010-2019.

OBJECTIVE: We described patterns and trends in ED use among adults with epilepsy in the United States. METHODS: Utilizing inpatient and ED discharge data from seven states, we conducted a cross-sectional analysis to identify adult ED visits diagnosed with epilepsy or seizures from 2010 to 2019. Using ED visit counts and estimates of state-level epilepsy prevalence, we calculated ED visit rates overall and by payer, condition, and year. RESULTS: Our data captured 304,935 ED visits with epilepsy as a primary or secondary diagnosis in 2019. Across the seven states, visit rates ranged between 366 and 726 per 1000 and were higher than rates for adults without epilepsy in all states but one. ED visit rates were highest among Medicare and Medicaid beneficiaries (vs commercial or self-pay). Adults with epilepsy were more likely to be admitted as inpatients. Visits for nervous system disorders were 6.3-8.2 times higher among people with epilepsy, and visits for mental health conditions were 1.2-2.6 times higher. Increases in ED visit rates from 2010 to 2019 among people with epilepsy exceeded increases among adults without by 6.0-27.3 percentage points. CONCLUSION: Adults with epilepsy visit the ED frequently and visit rates have been increasing over time. These results underscore the importance of identifying factors contributing to ED use and designing tailored interventions to improve ambulatory care quality.

Growth hormone receptor antagonist pegvisomant and its role in the medical therapy of growth hormone excess.

Pegvisomant is a growth-hormone (GH) receptor antagonist that prevents the formation of the active heterotrimer of the dimerised GH receptor and the GH molecule necessary for downstream signal transduction. Over the past 20 years, it has become a key therapeutic option for physicians treating syndromes of GH/IGF-1 excess. Sufficient longitudinal follow-up data suggest that it can be deemed both safe and effective. It is the drug with the greatest potential for achieving an amelioration of the biochemical effects of GH excess with a corresponding normalisation of IGF-1 levels; however, insufficient dose titration has lessened real-world therapeutic outcomes. Theoretical concerns about stimulating tumour growth have been resolved as this has not been observed, while derangement of liver enzymes and local skin-related adverse reactions may occur in a minority of the patients. It may be a particularly impactful medication for the treatment of children, young people, and those with inherited disorders of GH excess, where other treatment modalities often fail. Combination therapy of pegvisomant with first- and second-generation somatostatin receptor ligands or with dopamine agonists remains an ongoing area of interest and research. High cost remains a barrier to the use of pegvisomant in many settings.

Hexa-atom Pt Catalyst Fabricated by a Ligand Engineering Strategy for Efficient Hydrogen Oxidation Reaction.

Atomically precise supported nanocluster catalysts (APSNCs), which feature exact atomic composition, well-defined structures, and unique catalytic properties, offer an exceptional platform for understanding the structure-performance relationship at the atomic level. However, fabricating APSNCs with precisely controlled and uniform metal atom numbers, as well as maintaining a stable structure, remains a significant challenge due to uncontrollable dispersion and easy aggregation during synthetic and catalytic processes. Herein, we developed an effective ligand engineering strategy to construct a Pt6 nanocluster catalyst stabilized on oxidized carbon nanotubes (Pt6/OCNT). The structural analysis revealed that Pt6 nanoclusters in Pt6/OCNT were fully exposed and exhibited a planar structure. Furthermore, the obtained Pt6/OCNT exhibited outstanding acidic HOR performances with a high mass activity of 18.37 A ⋅ mgpt -1 along with excellent stability during a 24 h constant operation and good CO tolerance, surpassing those of the commercial Pt/C. Density functional theory (DFT) calculations demonstrated that the unique geometric and electronic structures of Pt6 nanoclusters on OCNT altered the hydrogen adsorption energies on catalytic sites and thus lowered the HOR theoretical overpotential. This work presents a new prospect for designing and synthesizing advanced APSNCs for efficient energy electrocatalysis.

Primary cell cultures from the single-chromosome ant Myrmecia croslandi.

The number of chromosomes varies tremendously across species. It is not clear whether having more or fewer chromosomes could be advantageous. The probability of non-disjunction should theoretically decrease with smaller karyotypes, but too long chromosomes should enforce spatial constraint for their segregation during the mitotic anaphase. Here, we propose a new experimental cell system to acquire novel insights into the mechanisms underlying chromosome segregation. We collected the endemic Australian ant Myrmecia croslandi, the only known species with the simplest possible karyotype of a single chromosome in the haploid males (and one pair of chromosomes in the diploid females), since males are typically haploid in hymenopteran insects. Five colonies, each with a queen and a few hundreds of workers, were collected in the Canberra district (Australia), underwent karyotype analysis to confirm the presence of a single pair of chromosomes in worker pupae, and were subsequently maintained in the laboratory in Paris (France). Starting from dissociated male embryos, we successfully conducted primary cell cultures comprised of single-chromosome cells. This could be developed into a unique model that will be of great interest for future genomic and cell biology studies related to mitosis.

Two newly established and mutually related subfamilies GH13_48 and GH13_49 of the α-amylase family GH13.

Currently, the main α-amylase family GH13 has been divided into 47 subfamilies in CAZy, with new subfamilies regularly emerging. The present in silico study was performed to highlight the groups, represented by the maltogenic amylase from Thermotoga neapolitana and the α-amylase from Haloarcula japonica, which are worth of creating their own new GH13 subfamilies. This enlarges functional annotation and thus allows more precise prediction of the function of putative proteins. Interestingly, those two share certain sequence features, e.g. the highly conserved cysteine in the second conserved sequence region (CSR-II) directly preceding the catalytic nucleophile, or the well-preserved GQ character of the end of CSR-VII. On the other hand, the two groups bear also specific and highly conserved positions that distinguish them not only from each other but also from representatives of remaining GH13 subfamilies established so far. For the T. neapolitana maltogenic amylase group, it is the stretch of residues at the end of CSR-V highly conserved as L-[DN]. The H. japonica α-amylase group can be characterized by a highly conserved [WY]-[GA] sequence at the end of CSR-II. Other specific sequence features include an almost fully conserved aspartic acid located directly preceding the general acid/base in CSR-III or well-preserved glutamic acid in CSR-IV. The assumption that these two groups represent two mutually related, but simultaneously independent GH13 subfamilies has been supported by phylogenetic analysis as well as by comparison of tertiary structures. The main α-amylase family GH13 has thus been expanded by two novel subfamilies GH13_48 and GH13_49. KEY POINTS: • In silico analysis of two groups of family GH13 members with characterized representatives • Identification of certain common, but also some specific sequence features in seven CSRs • Creation of two novel subfamilies-GH13_48 and GH13_49 within the CAZy database.

Utilizing Alcohol Septal Ablation for Mitigating Left Ventricular Outflow Tract Obstruction in Cardiac Amyloidosis: A Case Report.

Alcohol septal ablation (ASA) has been widely used in relieving the left ventricular outflow tract (LVOT) obstruction caused by hypertrophic obstructive cardiomyopathy (HOCM). There is limited data about the utility of ASA in cases of cardiac amyloidosis with LVOT obstruction. Our patient is 71-year-old male with a history of multiple myeloma complicated by cardiac amyloidosis and end-stage renal disease on hemodialysis who presented from the dialysis center due to hypotension. The patient was admitted to our hospital for further workup. He underwent echocardiography that showed severely elevated LVOT gradient pressures and the decision was made to proceed with ASA, which led to significant improvement in the LVOT gradient pressures and the patient being able to tolerate his dialysis sessions.

Covalent Bond Torsion-Enabled Unique Crystal-Phase Transformation of an Organic Semiconductor for Multicolor Light-Emitting Transistors.

High-mobility and color-tunable highly emissive organic semiconductors (OSCs) are highly promising for various optoelectronic device applications and novel structure-property relationship investigations. However, such OSCs have never been reported because of the great trade-off between mobility, emission color, and emission efficiency. Here, we report a novel strategy of molecular conformation-induced unique crystalline polymorphism to realize the high mobility and color-tunable high emission in a novel OSC, 2,7-di(anthracen-2-yl) naphthalene (2,7-DAN). Interestingly, 2,7-DAN has unique crystalline polymorphism, which has an almost identical packing motif but slightly different molecular conformation enabled by the small bond rotation angle variation between anthracene and naphthalene units. More remarkably, the subtle covalent bond rotation angle change leads to a big change in color emission (from blue to green) but does not significantly modify the mobility and emission efficiency. The carrier mobility of 2,7-DAN crystals can reach up to a reliable 17 cm2 V-1 s-1, which is rare for the reported high-mobility OSCs. Based on the unique phenomenon, high-performance light-emitting transistors with blue to green emission are simultaneously demonstrated in an OSC crystal. These results open a new way for designing emerging multifunctional organic semiconductors toward next-generation advanced molecular (atomic)-scale optoelectronics devices.

Unique molecular identifier-based amplicon sequencing of microhaplotypes for background noise mitigation.

Microhaplotypes (MHs), comprising two or more single-nucleotide polymorphisms in a short fragment, are promising forensic markers owing to their remarkable polymorphic nature. Several studies have demonstrated the utility of MHs through massively parallel sequencing (MPS). Nevertheless, the background noise level associated with MHs in MPS, which imposes a practical detection limit for the system, remains uninvestigated. Currently, unique molecular identifier (UMI) systems are known to effectively mitigate background noise by tracking original DNA molecules and facilitating PCR and MPS error corrections. Hence, this study aimed to design a UMI-based amplicon sequencing system, designated MH-UMIseq, which can amplify 46 MHs simultaneously and generate MPS libraries in four steps: barcoding PCR, nuclease reaction, boosting PCR, and indexing PCR. The performance of the MH-UMIseq system was evaluated using the Illumina NextSeq 550 and MiniSeq systems with 31 sets for 5 ng, 1 ng, and 200 pg of input DNA. The fgbio toolkit was used in conjunction with STRait Razor 3.0 and Visual Microhap to analyze the UMI data on MHs. The corresponding average not suppressed noise proportion of MH-UMIseq were 0.1 %, 0.3 %, and 0.7 % for 5 ng, 1 ng, and 200 pg of DNA, respectively, which substantially suppressed the background noise for more than 1 ng of DNA. Interestingly, the proportion of not suppressed noise in MH-UMIseq notably decreased as the amount of input DNA increased. The number of UMI families was proportional to the copy number of the template DNA and closely correlated with the system resolution. Therefore, the resolution of MH-UMIseq system is expected to be higher than that of conventional MPS for the deconvolution of mixtures containing more than 1 ng of DNA.

The Granular Retrosplenial Cortex Is Necessary in Male Rats for Object-Location Associative Learning and Memory, But Not Spatial Working Memory or Visual Discrimination and Reversal, in the Touchscreen Operant Chamber.

The retrosplenial cortex (RSC) is a hub of diverse afferent and efferent projections thought to be involved in associative learning. RSC shows early pathology in mild cognitive impairment and Alzheimer's disease (AD), which impairs associative learning. To understand and develop therapies for diseases such as AD, animal models are essential. Given the importance of human RSC in object-location associative learning and the success of object-location associative paradigms in human studies and in the clinic, it would be of considerable value to establish a translational model of object-location learning for the rodent. For this reason, we sought to test the role of RSC in object-location learning in male rats using the object-location paired-associates learning (PAL) touchscreen task. First, increased cFos immunoreactivity was observed in granular RSC following PAL training when compared with extended pretraining controls. Following this, RSC lesions following PAL acquisition were used to explore the necessity of the RSC in object-location associative learning and memory and two tasks involving only one modality: trial-unique nonmatching-to-location for spatial working memory and pairwise visual discrimination/reversal. RSC lesions impaired both memory for learned paired-associates and learning of new object-location associations but did not affect performance in either the spatial or visual single-modality tasks. These findings provide evidence that RSC is necessary for object-location learning and less so for learning and memory involving the individual modalities therein.

Single-Cell Sequencing of 3' RNA Transcripts.

Single-cell RNA sequencing (scRNA-seq) enables the measurement of RNA expressed from individual cells within a tissue or population. RNA expression profiles may be used to draw conclusions about cellular states, cell subtypes within the population, responses to perturbations, and cellular behavior in the context of disease. Here we describe a method for scRNA-seq via single-cell encapsulation and capture of the polyadenosine tails at the 3' end of mRNA transcripts combined with cell and molecular barcoding, allowing for the sequencing of 3' untranslated regions in order to identify expressed genes from a cell.

Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode.

The nucleosome remodeling and deacetylase (NuRD) complex plays a pivotal role in chromatin regulation and transcriptional repression. In mice, methyl-CpG binding domain 3 isoform C (MBD3C) interacts specifically with the histone H3 binding protein WD repeat-containing protein 5 (WDR5) and forms the WDR5-MBD3C/Norde complex. Despite the functional significance of this interaction on embryonic stem cell gene regulation, the molecular mechanism underlying MBD3C recognition by WDR5 remains elusive. Here, we determined the crystal structure of WDR5 in complex with the peptide (residues 40-51) derived from the MBD3C protein at a resolution of 1.9 Å. Structural analysis revealed that MBD3C utilizes a unique binding mode to interact with WDR5, wherein MBD3C Arg43 and Phe47 are involved in recognizing the WDR5-interacting (WIN) site and Tyr191-related B site on the small surface of WDR5, respectively. Notably, the binding induces a ∼91° rotation of WDR5 Tyr191, generating the hydrophobic B site. Furthermore, mutation experiments combined with isothermal titration calorimetry (ITC) assays confirmed the importance of both Arg43 and Phe47 in mediating WDR5 binding affinity. By determining structures of various peptides bound to WDR5, we demonstrated that the WDR5 WIN site and B site can be concurrently recognized by WIN motif peptides containing ''Arg-Cies/Ser-Arg-Val-Phe'' consensus sequence. Overall, this study reveals the structural basis for the formation of the WDR5-MBD3C subcomplex and provides new insights into the recognition mode of WDR5 for the WIN motif. Moreover, these findings shed light on structural-based designs of WDR5-targeted anti-cancer small molecule inhibitors or peptide-mimic drugs.

[Application of LU-tarjet congruent-arc technique in treatment of recurrent shoulder dislocation with huge glenoid defect].

Objective: To investigate the early effectiveness of the limited unique coracoid osteotomy suture button fixation Latarjet (LU-tarjet)-congruent-arc (CA) technique (LU-tarjet-CA) in treating recurrent shoulder dislocations with huge glenoid defect. Methods: The clinical data of 12 patients with recurrent shoulder dislocation and huge glenoid defect who met the selection criteria and treated with arthroscopic LU-tarjet-CA between January 2021 and December 2023 were retrospectively analyzed. The cohort included 8 males and 4 females, aged 20-40 years with an average age of 30.4 years. The range of glenoid bone loss was 30%-40%, with an average of 35.5%. The time from symptom onset to hospital admission ranged from 1 to 36 months, with an average of 18.5 months. The University of California Los Angeles (UCLA) score, American Association for Shoulder and Elbow Surgery (ASES) score, Walch-Duplay score, and Rowe score were used to evaluate shoulder function preoperatively and at 3, 6, and 12 months postoperatively. CT three-dimensional (3D) reconstruction was used to assess coracoid healing and plasticity at 3, 6, and 12 months postoperatively. Subjective satisfaction of patient was recorded at last follow-up. Results: All incisions healed by first intention, with no incision infection or nerve injury. All 12 patients were followed up 12 months. One patient developed Propionibacterium acnes infection within the joint postoperatively and recovered after initial arthroscopic debridement and anti-inflammatory treatment. At 3 months after operation, CT 3D-reconstruction showed 1 case of complete coracoid absorption; neither of these two patients experienced redislocation. The remaining patients exhibited partial coracoid absorption but displayed local reshaping, filling the preoperative defect area, and bony fusion between the coracoid and the glenoid. At last follow-up, 9 patients (75%) were very satisfied with the outcome, and 3 patients (25%) were satisfied; the satisfied patients experienced postoperative shoulder stiffness caused by suboptimal functional exercise but did not have impaired daily life activities. The UCLA score, ASES score, Walch-Duplay score, and Rowe score at 3, 6, and 12 months postoperatively were significantly better than preoperative scores, and each score improved further over time postoperatively, with significant differences between different time points ( P<0.05). Conclusion: The arthroscopic LU-tarjet-CA technique for treating recurrent shoulder dislocations with huge glenoid defect can achieve the surgical objective of bony blockade and filling bone defects to prevent shoulder dislocation, thereby improving patients' quality of life and shoulder joint function and stability.

Causal Structure Learning with Conditional and Unique Information Groups-Decomposition Inequalities.

The causal structure of a system imposes constraints on the joint probability distribution of variables that can be generated by the system. Archetypal constraints consist of conditional independencies between variables. However, particularly in the presence of hidden variables, many causal structures are compatible with the same set of independencies inferred from the marginal distributions of observed variables. Additional constraints allow further testing for the compatibility of data with specific causal structures. An existing family of causally informative inequalities compares the information about a set of target variables contained in a collection of variables, with a sum of the information contained in different groups defined as subsets of that collection. While procedures to identify the form of these groups-decomposition inequalities have been previously derived, we substantially enlarge the applicability of the framework. We derive groups-decomposition inequalities subject to weaker independence conditions, with weaker requirements in the configuration of the groups, and additionally allowing for conditioning sets. Furthermore, we show how constraints with higher inferential power may be derived with collections that include hidden variables, and then converted into testable constraints using data processing inequalities. For this purpose, we apply the standard data processing inequality of conditional mutual information and derive an analogous property for a measure of conditional unique information recently introduced to separate redundant, synergistic, and unique contributions to the information that a set of variables has about a target.

SLE: a cognitive step forward-a synthesis of rethinking theories, causality, and ignored DNA structures.

Systemic lupus erythematosus (SLE) is classified by instinctual classification criteria. A valid proclamation is that these formally accepted SLE classification criteria legitimate the syndrome as being difficult to explain and therefore enigmatic. SLE involves scientific problems linked to etiological factors and criteria. Our insufficient understanding of the clinical condition uniformly denoted SLE depends on the still open question of whether SLE is, according to classification criteria, a well-defined one disease entity or represents a variety of overlapping indistinct syndromes. Without rational hypotheses, these problems harm clear definition(s) of the syndrome. Why SLE is not anchored in logic, consequent, downstream interdependent and interactive inflammatory networks may rely on ignored predictive causality principles. Authoritative classification criteria do not reflect consequent causality criteria and do not unify characterization principles such as diagnostic criteria. We need now to reconcile legendary scientific achievements to concretize the delimitation of what SLE really is. Not all classified SLE syndromes are "genuine SLE"; many are theoretically "SLE-like non-SLE" syndromes. In this study, progressive theories imply imperative challenges to reconsider the fundamental impact of "the causality principle". This may offer us logic classification and diagnostic criteria aimed at identifying concise SLE syndromes as research objects. Can a systems science approach solve this problem?

[Design and Application of an IVD Reagent Management Information Systems Based on Unique Code].

The management of in vitro diagnostic (IVD) reagents in hospitals often faces issues such as the lack of a unified coding system, unclear consumption patterns, and unknown cost-to-income ratios. It is necessary to employ information systems to achieve comprehensive, detailed, and traceable management of IVD reagents. An information management system for IVD reagents based on unique coding is introduced, which integrates admission, acceptance, and consumption processes through unique codes. The system calculates the income per experimental item based on the consumption of IVD reagents and the charge for each experimental item. The system enhances the efficiency of the IVD reagent supply chain management and promotes detailed oversight of IVD reagent usage.

A Unique mRNA Vaccine Elicits Protective Efficacy against the SARS-CoV-2 Omicron Variant and SARS-CoV.

The highly pathogenic coronaviruses SARS-CoV-2 and SARS-CoV have led to the COVID-19 pandemic and SARS outbreak, respectively. The receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2, particularly the Omicron variant, has frequent mutations, resulting in the reduced efficiency of current COVID-19 vaccines against new variants. Here, we designed two lipid nanoparticle-encapsulated mRNA vaccines by deleting the mutant RBD of the SARS-CoV-2 Omicron variant (SARS2-S (RBD-del)) or by replacing this mutant RBD with the conserved and potent RBD of SARS-CoV (SARS2-S (SARS-RBD)). Both mRNA vaccines were stable at various temperatures for different time periods. Unlike SARS2-S (RBD-del) mRNA, SARS2-S (SARS-RBD) mRNA elicited effective T-cell responses and potent antibodies specific to both SARS-CoV-2 S and SARS-CoV RBD proteins. It induced strong neutralizing antibodies against pseudotyped SARS-CoV-2 and SARS-CoV infections and protected immunized mice from the challenge of the SARS-CoV-2 Omicron variant and SARS-CoV by significantly reducing the viral titers in the lungs after Omicron challenge and by completely preventing SARS-CoV-induced weight loss and death. SARS2-S (SARS-RBD)-immunized serum antibodies protected naïve mice from the SARS-CoV challenge, with its protective efficacy positively correlating with the neutralizing antibody titers. These findings indicate that this mRNA vaccine has the potential for development as an effective vaccine against current and future SARS-CoV-2 variants and SARS-CoV.

On the scientific credibility of paleoanthropology: Reply to Villmoare and Kimbel.

Smith and Wood reply to Villmoare and Kimbel regarding the scientific credibility of problems in paleoanthropology that require causal explanations for unique historical events.

Unusual Unique Renal Metastasis of Rectal Carcinoma.

Rectal cancer Is a Common malignant pathology; its usual spread in volves the liver and lungs. The occurrence of renal metastases is exceptional. CT scanning aims to evaluate extension and may incidentally reveal a renal mass, which can be better characterized through MRI and ultrasound. We describe a case of a solitary renal metastasis from rectal cancer and underscore the significant role of imaging in positively diagnosing this uncommon pathology.

Unique cartilage matrix-associated protein inhibits osteoclast differentiation by alleviating RANKL-induced reactive oxygen species.

Unique cartilage matrix-associated protein (UCMA) is a γ-carboxyglutamic acid-rich secretory protein primarily expressed in adult cartilage. UCMA promotes osteoblast differentiation and reduces high glucose-induced reactive oxygen species (ROS) production in osteoblasts; however, its role in osteoclasts remains unclear. Since Ucma is not expressed in osteoclasts, treatment with recombinant UCMA protein (rUCMA) was employed to investigate the effect of UCMA on osteoclasts. The rUCMA-treated osteoclasts exhibited significantly reduced osteoclast differentiation, resorption activity, and osteoclast-specific gene expression. Moreover, rUCMA treatment reduced RANKL-induced ROS production and increased the expression of antioxidant genes in osteoclasts. This study demonstrates that UCMA effectively inhibits RANKL-stimulated osteoclast differentiation and oxidative stress.