Integrating Phylogenies with Chronology to Assemble the Tree of Life.

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey of published literature shows that individual phylogenies are frequently restricted to specific taxonomic groups due to the expertise of investigators and molecular evolutionary considerations, resulting in any given species present in a minuscule fraction of phylogenies. We present a novel approach, called the chronological supertree algorithm (Chrono-STA), that can build a supertree of species from such data by using node ages in published molecular phylogenies scaled to time. Chrono-STA builds a supertree of organisms by integrating chronological data from molecular timetrees. It fundamentally differs from existing approaches that generate consensus phylogenies from gene trees with missing taxa, as Chrono-STA does not impute nodal distances, use a guide tree as a backbone, or reduce phylogenies to quartets. Analyses of simulated and empirical datasets show that Chrono-STA can combine taxonomically restricted timetrees with extremely limited species overlap. For such data, approaches that impute missing distances or assemble phylogenetic quartets did not perform well. We conclude that integrating phylogenies via temporal dimension enhances the accuracy of reconstructed supertrees that are also scaled to time.

Dynamic Metal-Coordinated Adhesive and Self-Healable Antifreezing Hydrogels for Strain Sensing, Flexible Supercapacitors, and EMI Shielding Applications.

Dynamic metal-coordinated adhesive and self-healable hydrogel materials have garnered significant attention in recent years due to their potential applications in various fields. These hydrogels can form reversible metal-ligand bonds, resulting in a network structure that can be easily broken and reformed, leading to self-healing capabilities. In addition, these hydrogels possess excellent mechanical strength and flexibility, making them suitable for strain-sensing applications. In this work, we have developed a mechanically robust, highly stretchable, self-healing, and adhesive hydrogel by incorporating Ca2+-dicarboxylate dynamic metal-ligand cross-links in combination with low density chemical cross-links into a poly(acrylamide-co-maleic acid) copolymer structure. Utilizing the reversible nature of the Ca2+-dicarboxylate bond, the hydrogel exhibited a tensile strength of up to ∼250 kPa and was able to stretch to 15-16 times its original length. The hydrogel exhibited a high fracture energy of ∼1500 J m-2, similar to that of cartilage. Furthermore, the hydrogel showed good recovery, fatigue resistance, and fast self-healing properties due to the reversible Ca2+-dicarboxylate cross-links. The presence of Ca2+ resulted in a highly conductive hydrogel, which was utilized to design a flexible resistive strain sensor. This hydrogel can strongly adhere to different substrates, making it advantageous for applications in flexible electronic devices. When adhered to human body parts, the hydrogel can efficiently detect limb movements. The hydrogel also exhibited excellent performance as a solid electrolyte for flexible supercapacitors, with a capacitance of ∼260 F/g at 0.5 A/g current density. Due to its antifreezing and antidehydration properties, this hydrogel retains its flexibility at subzero temperatures for an extended period. Additionally, the porous network and high water content of the hydrogel impart remarkable electromagnetic attenuation properties, with a value of ∼38 dB in the 14.5-20.5 GHz frequency range, which is higher than any other hydrogel without conducting fillers. Overall, the hydrogel reported in this study exhibits diverse applications as a strain sensor, solid electrolyte for flexible supercapacitors, and efficient material for electromagnetic attenuation. Its multifunctional properties make it a promising candidate for use in various fields as a state-of-the-art material.

Renal resistive index measurements by ultrasound in patients with liver cirrhosis: Magnitude and associations with renal dysfunction.

BACKGROUND: The hemodynamic alterations seen in liver cirrhosis lead to renal vasoconstriction, ultimately causing acute kidney injury (AKI). The renal resistive index (RRI) is the most common Doppler ultrasound variable for measuring intrarenal vascular resistance. AIM: To evaluate the association of the RRI with AKI in patients with liver cirrhosis and to identify risk factors for high RRI. METHODS: This was a prospective observational study, where RRI was measured using Doppler ultrasound in 200 consecutive hospitalized patients with cirrhosis. The association of RRI with AKI was studied. The receiver operating characteristic (ROC) curve analysis was utilized to determine discriminatory cut-offs of RRI for various AKI phenotypes. Multivariate analysis was conducted to determine the predictors of high RRI. RESULTS: The mean patient age was 49.08 ± 11.68 years, with the majority (79.5%) being male; the predominant etiology of cirrhosis was alcohol (39%). The mean RRI for the study cohort was 0.68 ± 0.09, showing a progressive increase with higher Child-Pugh class of cirrhosis. Overall, AKI was present in 129 (64.5%) patients. The mean RRI was significantly higher in patients with AKI compared to those without it (0.72 ± 0.06 vs 0.60 ± 0.08; P < 0.001). A total of 82 patients (41%) had hepatorenal syndrome (HRS)-AKI, 29 (22.4%) had prerenal AKI (PRA), and 18 (13.9%) had acute tubular necrosis (ATN)-AKI. The mean RRI was significantly higher in the ATN-AKI (0.80 ± 0.02) and HRS-AKI (0.73 ± 0.03) groups than in the PRA (0.63 ± 0.07) and non-AKI (0.60 ± 0.07) groups. RRI demonstrated excellent discriminatory ability in distinguishing ATN-AKI from non-ATN-AKI (area under ROC curve: 93.9%). AKI emerged as an independent predictor of high RRI (adjusted odds ratio [OR]: 11.52), and high RRI independently predicted mortality among AKI patients (adjusted OR: 3.18). CONCLUSION: In cirrhosis patients, RRI exhibited a significant association with AKI, effectively differentiated between AKI phenotypes, and predicted AKI mortality.

Bedside assessment of sarcopenia in hospitalized patients with liver cirrhosis: Magnitude and clinical implications.

BACKGROUND: Sarcopenia is associated with many adverse outcomes in patients with cirrhosis. The tools currently in use for assessing sarcopenia have numerous flaws. We evaluated the utility of portable ultrasonography and a dynamometer for the bedside assessment of sarcopenia and its implications in hospitalized cirrhosis patients. METHODS: A dynamometer was used to test the hand-grip strength (HGS) and ultrasound was used to measure the thickness of the forearm and quadriceps muscles. HGS value < 27 kg for men and < 16 kg for women was taken as significant according to the European Working Group on Sarcopenia in Older People (EWGSOP2) criteria. The lower normal limit of muscle mass (5th percentile) was determined on 100 matched healthy controls. RESULTS: According to the EWGSOP2 criteria and HGS values, the prevalence of sarcopenia and probable sarcopenia among 300 cirrhosis patients were 56% and 62.3%, respectively. HGS alone identified sarcopenia in 88.9% of patients, while overestimated it in 6.3% of cases. The prevalence rate of sarcopenic obesity was 11%. Compared to patients without sarcopenia, sarcopenic patients had more complications of cirrhosis such as ascites, variceal bleeding, hepatic encephalopathy, spontaneous bacterial peritonitis, sepsis, hepatorenal syndrome and refractory ascites. In-hospital (p = 0.037), three-month (p < 0.001), and six-month (p < 0.001) mortality rates were all higher among sarcopenic patients. On cox regression survival analysis, overall six-month mortality was significantly higher in sarcopenic patients compared to patients without sarcopenia (hazard ratio, 6.37; 95% confidence interval, 3.15-12.8, p < 0.001). CONCLUSION: Bedside assessment of sarcopenia using a portable ultrasound machine and a dynamometer detects liver cirrhosis patients with high risk of complications and mortality.

Collection efficiencies of cylindrical and plane parallel ionization chambers: analytical and numerical results and implications for experimentally determined correction factors.

Objectives.To derive a collection efficiency formula,fGauss, for cylindrical ionization chambers in pulsed radiation beams from a volume recombination model of Boaget al(1996Phys. Med. Biol.41885-97) including free electrons. To validatefGaussand a parallel plate chamber formulafexpusing an ion transport code and calculate changes in collection efficiencies caused by electric field charge screening at 0.1-100 mGy doses-per-pulse. And to determine collection efficienciesCE∞predicted at infinite voltage in the absence of avalanche effects by fitting scaled formulae to efficiencies computed for 100-400 V chamber voltages and 10 and 100 mGy doses-per-pulse.Approach.Calculations were performed for an idealized parallel plate chamber with 2 mm electrode separationd, and for an idealized cylindrical chamber with 0.5 and 2.333 mm inner and electrode radiirinandrout.Main results.fGaussandfexppredict the same collection efficiencies for cylindrical and parallel plate chambers satisfyingd2=(rout2-rin2)ln(rout/rin)/2, an equivalence condition met by the chambers studied. Without charge screening, efficiencies computed using the code equalledfGaussandfexp. With screening, efficiencies changed by ⩽0.03%, ⩽1.1% and ⩽21.3% at 1, 10 and 100 mGy doses-per-pulse, and differed between the chambers by ⩽0.9% and ⩽19.6% at ⩽10 and 100 mGy dose-per-pulse. For fits offexpandfGauss,CE∞values were ⩽1.2% and ⩽17.6% from unity at 10 and 100 mGy per pulse respectively, closer than for other formulae tested.Significance.Allowing for screening,fGaussandfexpdescribed computed collection efficiencies to within 0.03%, 1.1% and 21.3% at doses-per-pulse ⩽1, 10 and 100 mGy. Equivalence of the two chambers broke down at 100 mGy per pulse. Departures ofCE∞values from unity suggest that collection efficiencies determined experimentally by fittingfGaussorfexpto readings made at multiple voltages will be accurate to within 1.2% and 17.6% at 10 and 100 mGy per pulse respectively.

Advancements in unravelling the fundamental function of the ATAD3 protein in multicellular organisms.

ATPase family AAA domain containing protein 3, commonly known as ATAD3 is a versatile mitochondrial protein that is involved in a large number of pathways. ATAD3 is a transmembrane protein that spans both the inner mitochondrial membrane and outer mitochondrial membrane. It, therefore, functions as a connecting link between the mitochondrial lumen and endoplasmic reticulum facilitating their cross-talk. ATAD3 contains an N-terminal domain which is amphipathic in nature and is inserted into the membranous space of the mitochondria, while the C-terminal domain is present towards the lumen of the mitochondria and contains the ATPase domain. ATAD3 is known to be involved in mitochondrial biogenesis, cholesterol transport, hormone synthesis, apoptosis and several other pathways. It has also been implicated to be involved in cancer and many neurological disorders making it an interesting target for extensive studies. This review aims to provide an updated comprehensive account of the role of ATAD3 in the mitochondria especially in lipid transport, mitochondrial-endoplasmic reticulum interactions, cancer and inhibition of mitophagy.

Unveiling silicon-mediated cadmium tolerance mechanisms in mungbean (Vigna radiata (L.) Wilczek): Integrative insights from gene expression, antioxidant responses, and metabolomics.

Cadmium (Cd), one of the most phytotoxic heavy metals, is a major contributor to yield losses in several crops. Silicon (Si) is recognized for its vital role in mitigating Cd toxicity, however, the specific mechanisms governing this mitigation process are still not fully understood. In the present study, the effect of Si supplementation on mungbean (Vigna radiata (L.) Wilczek) plants grown under Cd stress was investigated to unveil the intricate pathways defining Si derived stress tolerance. Non-invasive leaf imaging technique revealed improved growth, biomass, and photosynthetic efficiency in Si supplemented mungbean plants under Cd stress. Further, physiological and biochemical analysis revealed Si mediated increase in activity of glutathione reductase (GR), ascorbate peroxidase (APX), and catalase (CAT) enzymes involved in reactive oxygen species (ROS) metabolism leading to mitigation of cellular damage and oxidative stress. Untargeted metabolomic analysis using liquid chromatography coupled with mass spectrometry (LC-MS/MS) provided insights into Si mediated changes in metabolites and their respective pathways under Cd stress. Alteration in five different metabolic pathways with major changes in flavanols and flavonoids biosynthesis pathway which is essential for controlling plants antioxidant defense system and oxidative stress management were observed. The information reported here about the effects of Si on photosynthetic efficiency, antioxidant responses, and metabolic changes will be helpful in understanding the Si-mediated resistance to Cd stress in plants.

Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning.

Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.

A Plasmodium falciparum genetic cross reveals the contributions of pfcrt and plasmepsin II/III to piperaquine drug resistance.

Piperaquine (PPQ) is widely used in combination with dihydroartemisinin as a first-line treatment against malaria. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multidrug-resistant KEL1/PLA1 lineage isolate (KH004) and a drug-susceptible Malawian parasite (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and multiple copies of pm2/3. We recovered 104 unique recombinant parasites and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3. We performed a detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes with these progenies, including PPQ survival assay, area under the dose response curve, and a limited point IC50. We find that inheritance of the KH004 pfcrt allele is required for reduced PPQ sensitivity, whereas copy number variation in pm2/3 further decreases susceptibility but does not confer resistance in the absence of additional mutations in pfcrt. A deep investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background to a range of PPQ-related traits. Additionally, we find that the resistance phenotype associated with parasites inheriting the G367C substitution in pfcrt is consistent with previously validated PPQ resistance mutations in this transporter.IMPORTANCEResistance to piperaquine, used in combination with dihydroartemisinin, has emerged in Cambodia and threatens to spread to other malaria-endemic regions. Understanding the causal mutations of drug resistance and their impact on parasite fitness is critical for surveillance and intervention and can also reveal new avenues to limiting the evolution and spread of drug resistance. An experimental genetic cross is a powerful tool for pinpointing the genetic determinants of key drug resistance and fitness phenotypes and has the distinct advantage of quantifying the effects of naturally evolved genetic variation. Our study was strengthened since the full range of copies of KH004 pm2/3 was inherited among the progeny clones, allowing us to directly test the role of the pm2/3 copy number on resistance-related phenotypes in the context of a unique pfcrt allele. Our multigene model suggests an important role for both loci in the evolution of this multidrug-resistant parasite lineage.

Blocking Oncostatin M receptor abrogates STAT3 mediated integrin signaling and overcomes chemoresistance in ovarian cancer.

Chemotherapy such as cisplatin is widely used to treat ovarian cancer either before or after surgical debulking. However, cancer relapse due to chemotherapy resistance is a major challenge in the treatment of ovarian cancer. The underlying mechanisms related to chemotherapy resistance remain largely unclear. Therefore, identification of effective therapeutic strategies is urgently needed to overcome therapy resistance. Transcriptome-based analysis, in vitro studies and functional assays identified that cisplatin-resistant ovarian cancer cells express high levels of OSMR compared to cisplatin sensitive cells. Furthermore, OSMR expression associated with a module of integrin family genes and predominantly linked with integrin αV (ITGAV) and integrin ß3 (ITGB3) for cisplatin resistance. Using ectopic expression and knockdown approaches, we proved that OSMR directly regulates ITGAV and ITGB3 gene expression through STAT3 activation. Notably, targeting OSMR using anti-OSMR human antibody inhibited the growth and metastasis of ovarian cancer cells and sensitized cisplatin treatment. Taken together, our results underscore the pivotal role of OSMR as a requirement for cisplatin resistance in ovarian cancer. Notably, OSMR fostered the expression of a distinct set of integrin genes, which in turn resulted into a crosstalk between OSMR and integrins for signaling activation that is critical for cisplatin resistance. Therefore, targeting OSMR emerges as a promising and viable strategy to reverse cisplatin-resistance in ovarian cancer.

Impact of Microplastics on Pregnancy and Fetal Development: A Systematic Review.

Microplastic (MP) pollution is a growing global concern because of its potential to impair human health, particularly with regard to fetal development. However, the origins of prenatal MP exposure and its effects on fetal development have not been well studied. This study aimed to provide a systematic review of the literature regarding the impact of microplastics on pregnancy and fetal development. PubMed, Embase, ScienceDirect, Web of Science, Scopus, and Google Scholar were searched from 2010 until March 2024. Original publications exploring the impact of microplastics on pregnancy and fetal development were included in the study. After selecting papers, two independent reviewers extracted data regarding study characteristics, microplastics identified, and reproductive impacts. The quality of studies was assessed using the Critical Appraisal Checklists for Studies created by the Joanna Briggs Institute (JBI). Twelve studies, including 234 subjects, were selected from a total of 2,809 citations for the final qualitative analysis. Articles were published between 2021 and 2024, and most were conducted in China. The results of the included studies confirmed the existence of microplastics with varying sizes (2.1 to 100 micrometers) in the placenta and the fetal body. Studies revealed correlations between lifestyle choices and the presence of microplastics in the placenta. They also reported correlations between the level of microplastics and diminished microbiome diversity, reduced birthweights, affected gestational age, and fetal growth and development. Microplastics may be detrimental to a developing fetus during pregnancy. Nonetheless, more thorough research is required to comprehend the impact of microplastic exposure on pregnancy and fetal development.

Hepatogenous Diabetes as Compared to Type-2 Diabetes Mellitus and Non-diabetes in Patients With Liver Cirrhosis: Magnitude, Characteristics, and Implications.

Aim: Hepatogenous diabetes (HD) is frequently underestimated among cirrhosis patients. The current study assessed the magnitude, clinical characteristics, and implications of HD in cirrhosis patients as compared to the patients with type-2 diabetes mellitus (T2DM) and non-diabetes (ND) cirrhosis. Methods: In a prospective observational study, 338 consecutive eligible cirrhosis patients were screened for diabetes mellitus. A 2-hour oral glucose tolerance test (OGTT) was used to detect HD. The clinical characteristics, complications, and outcomes were ascertained and compared amongst HD, T2DM, and ND patients. Results: In the final study cohort of 316 patients, the proportion of HD, T2DM, and ND was 22.5% (n = 71), 26.3% (n = 83), and 51.3% (n = 162), respectively. HD was the predominant form of diabetes (68.9%) in Child-Pugh class-C cirrhosis. The majority (73%) of HD patients had abnormal OGTT without fasting hyperglycaemia. A lower cut-off of 98.5 mg/dl for fasting blood glucose had a modest sensitivity (72%) and specificity (75%) for predicting HD. In comparison to T2DM patients, HD patients were younger, leaner, and had more advanced cirrhosis. In comparison to ND patients, HD patients were leaner but had higher glycemic indices, serum cholesterol, and arterial ammonia levels. During a median follow-up period of 12 (03-21) months, the frequency of hepatic encephalopathy and variceal haemorrhage were higher in HD and T2DM patients compared to that in the ND group. Conclusions: HD is prevalent in about one fifth of cirrhosis patients. It differs from T2DM and ND in a number of ways, and has association with complications of cirrhosis.

Autologous Stem Cell Transplantation in Adult Hodgkin Lymphoma at a Tertiary Care Center in India: Analysis of Outcomes and Prognostic Factors.

High-dose chemotherapy and autologous stem cell transplant (ASCT) is the standard of care treatment in relapsed/refractory Hodgkin lymphoma (rrHL). Published long-term follow-up data concerning this modality from the Indian subcontinent is lacking. In this retrospective study, the data on adults (> 16 years) with biopsy-confirmed rrHL who were autografted from 1 January 2000 to 31 December 2021 at our transplant unit were analyzed. Progression-free survival (PFS) was defined as time from transplant to disease progression or death due to any cause. Overall survival (OS) was determined from date of transplant to date of death due to any cause. Overall, 134 patients with Hodgkin lymphoma underwent ASCT. At a median follow-up of 38.2 (range, 0.1-240) months, 5 years PFS was 45.3% (95% CI 35.4-54.4). The probability of OS at 5 years was 60.5% (95% CI 49.6-69.6). Eleven (8.2%) patients suffered transplant-related mortality by 100 days. Post-transplant persistent disease, pre-transplant serum hypoalbuminemia (< 3.5 g/dl) and chemo-resistance (< PR after last salvage regimen) of tumour at transplant were independent prognostic factors associated with worse PFS in multivariable analysis. Likewise, age ≥ 30 years, ECOG performance status ≥ 1 and residual disease after transplantation correlated with inferior OS. Long-term outcomes of rrHL patients undergoing ASCT in India match those from the developed world in the era of peripheral blood stem cell transplantation. Pre-transplant performance status, chemo-sensitivity of disease, serum albumin and post-transplant remission status determined survival in our cohort. Supplementary Information: The online version contains supplementary material available at 10.1007/s12288-023-01690-x.

Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet.

MAIN CONCLUSION: Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.

Uncovering sources, distribution, and seasonal patterns of trace element deposition: the elemental puzzle of the western Himalayas.

The transport and deposition of atmospheric pollutants in the Himalayas have a adverse impact on the climate, cryosphere, ecosystem, and monsoon patterns. Unfortunately, there is a insufficiency of data on trace element concentrations and behaviors in the high-altitude Himalayan region, leading to limited research in this area. This study presents a comprehensive and detailed comprehension of trace element deposition, its spatial distribution, seasonal variations, and anthropogenic signals in the high-altitude Kashmir region of the Western Himalayas. Our investigation involved the analysis of 10 trace elements (Al, Cr, Mn, Fe, Co, Ni, Cu, Zn, Cd, and Pb) in glacier ice, snow pits, surface snow, and rainwater collected at various sites including Kolahoi, Thajwas, Pahalgam (Greater Himalayan ranges), and Kongdori and Shopian (Pir Panjal Ranges) during 2021. The study reveals distinct ranges of concentrations for the trace elements at different sampling sites. Our analysis of trace element concentration depth profiles in snow pits reveals seasonal fluctuations during the deposition year. The highest concentrations were found in the autumn (below 20 cm) and summer (top layer), compared to the winter concentration (10-20 cm). The high enrichment factors (EFs) suggest the severity of human-induced trace metal deposition in the western Himalayan region, relative to surrounding regions. Surprisingly, the concentrations and EFs of trace elements showed seasonal contradictions, with lower concentration values and higher EFs during the non-monsoon season and vice versa. A source apportionment analysis using the positive matrix factorization (PMF) technique identified five sources of trace element deposition in the region, including crustal sources (32.33%), coal combustion (15.62%), biomass burning (17.63%), traffic emission (18.8%), and industrial sources (15.6%). Additionally, the study incorporated backward trajectories coupled with δ18O using the NOAA HYSPLIT model to estimate moisture sources in the region, which suggests atmospheric pollutants predominately deposited from the large-scale atmospheric circulation from westerlies (75%) during non-monsoon season. These findings underscore the urgent need for enhanced monitoring and research efforts in the future.

Acid mine drainage from coal mines in the eastern Himalayan sub-region: Hydrogeochemical processes, seasonal variations and insights from hydrogen and oxygen stable isotopes.

Uncontrolled coal mining using non-scientific methods has presented a major threat to the quality of environment, particularly the water resources in eastern himalayan sub-region of India. Water bodies in the vicinity of mining areas are contaminated by acid mine drainage (AMD) that is released into streams and rivers. This study attempted to assess the impact of AMD, deciphering hydrogeochemical processes, seasonal fluctuations, and stable isotope features of water bodies flowing through and around coal mining areas. Self-organizing maps (SOMs) used to separate and categorize AMD, AMD-impacted and non-AMD impacted water from the different study locations for two sampling seasons revealed four clusters (C), with C1 and C2 impacted by AMD, C3 and C4 showing negligible to no impact of AMD. AMD impacted water was SO42- - Mg2+- Ca2+ hydrochemical type with sulphide oxidation and evaporation dominating water chemistry, followed by silicate weathering during both the sampling seasons. Water with negligible-to-no AMD-impact was Mg2+- Ca2+- SO42- to Ca2+ - HCO3- to mixed hydrochemical type with rock weathering and dissolution, followed by ion exchange as major factors controlling water chemistry during both the sampling seasons. Most of physicochemical parameters of C1 and C2 exceeded the prescribed limits, whereas in C3 and C4 water samples, parameters were found within the prescribed limits. Stable isotopes of hydrogen (δ2H) and oxygen (δ18O) during post-monsoon (PoM) varied between -41.04 ‰ and -29.98 ‰, and -6.60 ‰ to -3.94 ‰; and during pre-monsoon (PrM) varied between -58.18 ‰ and - 33.76 ‰ and -8.60 ‰ to -5.46 ‰. Deuterium excess (d-excess) ranged between 1.57 ‰ and 12.47 ‰ during PoM and 5.70 ‰ to 15.17 ‰ during PrM season. The stable isotopes analysis revealed that evaporation, mineral dissolution and mixing with rainwater are the key factors in study area.

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics.

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.

Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning.

Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, infer organismal relationships with high statistical confidence. But, these relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.

Unlocking growth potential: Synergistic potassium fertilization for enhanced yield, nutrient uptake, and energy fractions in Chinese cabbage.

The implementation of integrated potassium management presents a viable approach for augmenting plant growth, yield, and nutrient uptake while enhancing soil nutrient availability. A field experiment was executed during the rabi season of 2020, employing a randomized complete block design encompassing eight treatments involving standard (100%) and reduced (75% and 50%) rates of the recommended dose of potassium (RDK) administered through muriate of potash (MOP). Treatments included variations in the incorporation/exclusion of plant growth-promoting rhizobacteria (PGPR), farmyard manure (FYM) at 25% of potassium recommendation, and foliar application of nano potash. The use of 100% RDK +25% K augmentation through FYM + PGPR and nano K fertilizer spray at 25 and 40 DAS (T8) exhibited significant enhancements in green fodder yield (64.0 ± 2.2 t ha-1) over control with no potassium application (47.3 ± 3.7 t ha-1) and found at par with and 75% RDK + 25% K augmentation through FYM + PGPR and nano K fertilizer spray at 25 and 40 DAS (T7). These treatments yielded maximum percent increase for plant height (34.9%), leaf count (38.5%), leaf dimensions (28.8-31.5%), stem girth (25.84%), root volume (27.0%), and root length (37.64%), observed at the harvest stage compared to control (T1-no potassium application). The treatment T8 was on par with T7 and recorded highest uptake of macro (N, P, and K) and micro (Zn, Fe, Cu, and Mn) nutrients. While soil parameters such as available nitrogen and potassium levels were notably increased through the application of treatment T7 across various treatment combinations and found significantly superiority over treatment T8. Multivariate analysis also highlighted treatment T7 is more efficient in maintaining sustainability. Hence, based on the present findings it can be concluded that application of 75% RDK +25% K augmentation through FYM + PGPR and nano K fertilizer spray at 25 and 40 DAS (T7) can be recommended for achieving enhanced productivity and soil fertility improvement within agricultural systems.

Assessment of Potentially Malignant Disorders among Men and Women in South Bihar Population.

Oral cancer is detected in 270,000 people per annum or around 3% of all malignancies. It ranks sixth among males and twelve among females in terms of prevalence. Mostly, all oral squamous cell carcinomas (OSCC) are responsible for 92-95% of cases. Oral carcinoma starts five years before the average age of PMD patients, who range in age from 5th to 6th decade of life. Thus, the goal of this study is to identify any relevant risk factors and assess the incidence of oral possibly malignant disorders in both men and women living in rural Bhojpur District, Bihar. A cross-sectional study has been carried out at the Sadar Hospital in Bhojpur by surveying volunteers at various oral health screening and treatment camps held from January 2022 to July 2022. A pre-validated questionnaire adapted and modified from Kumar S et al. was utilized to collect data in a qualitative interview. It was discovered that (17%) of all people had an oral possibly malignant disease. OSMF was the lesion with the greatest prevalence (7%) and lichen planus having the smallest prevalence (1%). Malignancy frequently develops from oral potential malignant diseases. Diabetes and BMI were inversely related, which is expected provided the socioeconomic position.