bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen
Authors: Castillo Andreina I , Almeida Rodrigo P P 
Published: March 2021

Abstract
Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, core vs accessory, and recombinant vs non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene-level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.
A novel hybrid liquefied natural gas process with absorption refrigeration integrated with molten carbonate fuel cell
Authors: Mehrpooya Mehdi , Bahramian Parimah , Pourfayaz Fathollah , Katooli Hadi , Delpisheh Mostafa 
Published: March 2021

Abstract
The production of liquefied natural gas (LNG) is a high energy-consuming process. The study of ways to reduce energy consumption and consequently to reduce operational costs is imperative. Toward this purpose, this study proposes a hybrid system adopting a mixed refrigerant for the liquefaction of natural gas that is precooled with an ammonia/water absorption refrigeration (AR) cycle utilizing the exhaust heat of a molten carbonate fuel cell, 700°C and 2.74 bar, coupled with a gas turbine and a bottoming Brayton super-critical carbon dioxide cycle. The inauguration of the ammonia/water AR cycle to the LNG process increases the cooling load of the cycle by 10%, providing a 28.3-MW cooling load duty while having a 0.45 coefficient of performance. Employing the hybrid system reduces energy consumption, attaining 85% overall thermal efficiency, 53% electrical efficiency and 35% fuel cell efficiency. The hybrid system produces 6300 kg.mol.h−1 of LNG and 146.55 MW of electrical power. Thereafter, exergy and sensitivity analyses are implemented and, accordingly, the fuel cell had an 83% share of the exergy destruction and the whole system obtained a 95% exergy efficiency.
Phenotypic and genotypic antimicrobial resistance in clinical anaerobic isolates from India
Authors: Sood Anshul , Ray Pallab , Angrup Archana 
Published: March 2021

Abstract

Background
Antimicrobial resistance (AMR) in anaerobes remains a neglected field. The laborious procedures, non-compliance with the standard methodology and differences in interpretive breakpoints add variation in resistance data.

Objectives
To assess the phenotypic and genotypic resistance among clinically important anaerobes to six antibiotics frequently used as empirical therapy for anaerobic infections.

Methods
A total of 150 anaerobic isolates were recovered from clinical specimens. The antimicrobial susceptibility was determined by the breakpoint agar dilution method as per CLSI guidelines. The presence of genes encoding resistance to metronidazole (nim gene), imipenem (cfiA gene) and mobilizable insertion sequence (IS) elements was detected to comprehend their association with phenotypic resistance.

Results
This is a first study of its kind from the Indian subcontinent looking at the AMR and associated genes in anaerobes. Resistance to metronidazole, clindamycin, imipenem, piperacillin/tazobactam and cefoxitin was 32.6%, 42.6%, 0.6%, 38% and 35.3%, respectively. No resistance was observed to chloramphenicol. The nim gene was detected in 24.6% of isolates, of which 70.2% were resistant by phenotype. On sequencing, the PCR products of six random nim genes showed a close similarity to nimE of Bacteroides fragilis with 99% nucleotide and 100% amino acid sequence similarity. The cfiA gene, associated with imipenem resistance, was detected in 16% of isolates.

Conclusions
The possibility of isolates carrying AMR genes to become resistant to antibiotics by acquisition of IS elements mandates attention to periodically monitor the resistance patterns and geographic distribution of these genes and IS elements to understand the trends of AMR in anaerobes.
Temporal kinetics of bovine mammary IgG secretion into colostrum and transition milk
Authors: Schalich Kasey M , Reiff Olivia M , Nguyen Blake T , Lamb Cassandra L , Mondoza Cecilia R , Selvaraj Vimal 
Published: March 2021

AbstractNeonatal calf survival and health is predominantly dependent on sufficient consumption of immunoglobulin G (IgG) and the resulting transfer of passive immunity (TPI). In this study, we investigate the potential for continued IgG secretion and temporal kinetics of mammary IgG output in sequential milkings performed at 0, 4, 16, 28, 40, and 52 hr postcalving in Holstein dairy cows. For colostrum (0 hr), we also scrutinize the relationships between IgG concentration, volume, refractometer readings (˚Bx values, Brix) and concentration of sugars (lactose and glucose). Mammary transcripts postpartum (0 hr) indicated that active IgG secretion continues beyond the first milking (colostrum; n = 4 to 5). IgG measurements at the different timepoints indicated that colostrum represents only 25.1% of the total IgG produced across the 6 sequential milking timepoints, with a substantial 48.9% being secreted into transition milk over the next 3 timepoints (4-, 6-, and 28-hr) combined. The differences on the basis of IgG concentrations across 0-, 4-, and 16-hr milking timepoints were not statistically significant (P = 0.1522; n = 9). For colostrum, volume remained highly variable, even with induced let-down prior to milking (n = 27). Nonetheless, colostrum IgG secretion was significantly co-regulated with volume (R2 = 0.915; P &lt; 0.001; n = 18), an association that was stronger than that measured for lactose (R2 = 0.803; P &lt; 0.001; n = 18) and glucose (R2 = 0.467; P = 0.002; n = 17). Comparing colostrum ˚Bx values to absolute IgG concentrations showed no correlation (R2 = 0.127; P = 0.07; n = 27); biochemical separation of colostrum components indicated that both proteins and nonprotein solutes could affect ˚Bx values (P &lt; 0.0001 for both; n = 5). This suggests that ˚Bx values do not reasonably indicate IgG concentration to serve as a measure of “colostrum quality.” Additionally, our finding that early transition milk (4-, 6-, and 28-hr) can contribute substantially more IgG than colostrum forces a rethink of existing feeding paradigms and means to maximize TPI in calves. Collectively, our results reveal the remarkable value of early transition milk and caveats to colostrum assessments that could advance application in enhancing neonatal calf health.
Projecting the Global Potential Distribution of Cydia pomonella (Lepidoptera: Tortricidae) Under Historical and RCP4.5 Climate Scenarios
Authors: Guo Siwei , Ge Xuezhen , Zou Ya , Zhou Yuting , Wang Tao , Zong Shixiang 
Published: March 2021

Abstract
The codling moth Cydia pomonella (L.) (Lepidoptera: Tortricidae) is a destructive pest of apple (Malus domestica (Rosales: Rosaceae)), pear (Pyrus spp. (Rosales: Rosaceae)), and other pome tree fruits; outbreaks cause significant ecological and economic losses. In this study, we used CLIMEX model to predict and evaluate the global risk of C. pomonella based on historical climate data (1989–2018) and simulated future climate data (2071–2100) under the RCP4.5 scenarios. Cydia pomonella exhibited a wide distribution under both historical and future climate conditions. Climate change is predicted to expand the northern boundary of the potential distribution from approximately 60°N to 75°N. Temperature was the most dominant factor in climatic suitability for the pest. Combinations of multiple meteorological factors (relative humidity and precipitation) associated with a failure to break diapause in certain regions also affect suitability, particularly in northern South America and central Africa. Irrigation only had a slight impact on species favorability in some areas. The projections established in our study present insight into the global potential suitability of C. pomonella under climate change scenarios by the end of the 21st century. Farmers should be aware of the risk associated with the pest based on the results, which would provide guidance for quarantine agencies and trade negotiators worldwide.
Cavitary Coccidioidomycosis: Impact of azole antifungal therapy
Authors: Panicker Renni R , Bartels Helen C , Gotway Michael B , Ampel Neil M , Buras Matthew R , Lim Elisabeth S , Blair Janis E 
Published: March 2021

Abstract

Approximately 5 to 15% of patients with pulmonary coccidioidomycosis subsequently develop pulmonary cavities. These cavities may resolve spontaneously over a number of years; however, some cavities never close, and a small proportion causes complications such as hemorrhage, pneumothorax or empyema. The impact of azole antifungal treatment on coccidioidal cavities has not been studied. Because azoles are a common treatment for symptomatic pulmonary coccidioidomycosis, we aimed to assess the impact of azole therapy on cavity closure. From January 1, 2004, through December 31, 2014, we retrospectively identified 313 patients with cavitary coccidioidomycosis and excluded 42 who had the cavity removed surgically, leaving 271 data sets available for study. Of the 271 patients, 221 (81.5%) received azole therapy during 5-year follow-up; 50 patients did not receive antifungal treatment. Among the 271 patients, cavities closed in 38 (14.0%). Statistical modeling showed that cavities were more likely to close in patients in the treated group than in the nontreated group (hazard ratio, 2.14 [95% CI: 1.45–5.66]). Cavities were less likely to close in active smokers than nonsmokers (11/41 [26.8%] vs 97/182 [53.3%]; P = 0.002) or in persons with than without diabetes (27/74 [36.5%] vs 81/149 [54.4%]; P = 0.01).We did not find an association between cavity size and closure. Our findings provide rationale for further study of treatment protocols in this subset of patients with coccidioidomycosis.

Lay Summary
Coccidioidomycosis, known as valley fever, is a fungal infection that infrequently causes cavities to form in the lungs, which potentially results in long-term lung symptoms. We learned that cavities closed more often in persons who received antifungal drugs, but most cavities never closed completely.
Norovirus in Cancer Patients: A Review
Authors: Kondapi Divya Samantha , Ramani Sasirekha , Estes Mary K , Atmar Robert L , Okhuysen Pablo C 
Published: March 2021

AbstractNorovirus (NoV) is the leading cause of viral-related diarrhea in cancer patients, in whom it can be chronic, contributing to decreased quality of life, interruption of cancer care, malnutrition, and altered mucosal barrier function. Immunosuppressed cancer patients shed NoV for longer periods of time than immunocompetent hosts, favoring quasispecies development and emergence of novel NoV variants. While nucleic acid amplification tests (NAATs) for NoV diagnosis have revolutionized our understanding of NoV burden of disease, not all NAATs provide information on viral load or infecting genotype. There is currently no effective antiviral or vaccine for chronic NoV infections. Screening for inhibitors of NoV replication in intestinal organoid culture models and creation of NoV-specific adoptive T cells are promising new strategies to develop treatments for chronic NoV in immunosuppressed patients. Herein we summarize data on the epidemiology, clinical manifestations, diagnostic challenges, and treatment of NoV infection in patients with cancer.
The microtubule-associated protein WDL4 modulates auxin distribution to promote apical hook opening in Arabidopsis
Authors: Deng Jia , Wang Xiangfeng , Liu Ziqiang , Mao Tonglin 
Published: March 2021

Abstract
The unique apical hook in dicotyledonous plants protects the shoot apical meristem and cotyledons when seedlings emerge through the soil. Its formation involves differential cell growth under the coordinated control of plant hormones, especially ethylene and auxin. Microtubules are essential players in plant cell growth that are regulated by multiple microtubule-associated proteins (MAPs). However, the role and underlying mechanisms of MAP-microtubule modules in differential cell growth are poorly understood. In this study, we found that the previously uncharacterized Arabidopsis MAP WAVE-DAMPENED2-LIKE4 (WDL4) protein plays a positive role in apical hook opening. WDL4 exhibits a temporal expression pattern during hook development in dark-grown seedlings that is directly regulated by ethylene signaling. WDL4 mutants showed a delayed hook opening phenotype while overexpression of WDL4 resulted in enhanced hook opening. In particular, wdl4-1 mutants exhibited stronger auxin accumulation in the concave side of the apical hook. Furthermore, the regulation of the auxin maxima and trafficking of the auxin efflux carriers PIN-FORMED1 (PIN1) and PIN7 in the hook region is critical for WDL4-mediated hook opening. Together, our study demonstrates that WDL4 positively regulates apical hook opening by modulating auxin distribution, thus unraveling a mechanism for MAP-mediated differential plant cell growth.
Across the great divide: revision of the genusEupetaurus(Sciuridae: Pteromyini), the woolly flying squirrels of the Himalayan region, with the description of two new species
Authors: Jackson Stephen M , Li Quan , Wan Tao , Li Xue-You , Yu Fa-Hong , Gao Ge , He Li-Kun , Helgen Kristofer M , Jiang Xue-Long 
Published: March 2021

AbstractThe woolly flying squirrel, Eupetaurus cinereus, is among the rarest and least studied mammals in the world. For much of the 20th century it was thought to be extinct, until it was rediscovered in 1994 in northern Pakistan. This study outlines the first taxonomic and biogeographical review of the genus Eupetaurus, which until now has contained only a single species. Careful review of museum specimens and published records of Eupetaurus demonstrates that the genus occurs in three widely disjunct areas situated on the western (northern Pakistan and north-western India), north-central (south-central Tibet, northern Sikkim and western Bhutan) and south-eastern margins (north-western Yunnan, China) of the Himalayas. Taxonomic differentiation between these apparently allopatric populations of Eupetaurus was assessed with an integrative approach involving both morphological examinations and molecular phylogenetic analyses. Phylogenetic reconstruction was implemented using sequences of three mitochondrial [cytochrome b (Cytb), mitochondrially encoded 12S and 16S ribosomal RNA (12S, 16S)] and one nuclear [interphotoreceptor retinoid-binding protein (IRBP)] gene fragment. Morphological assessments involved qualitative examinations of features preserved on museum skins and skulls, supplemented with principal components analysis of craniometric data. Based on genetic and morphological comparisons, we suggest that the three widely disjunct populations of Eupetaurus are each sufficiently differentiated genetically and morphologically to be recognized as distinct species, two of which are described here as new.
Persistent Fetal Kidney Lobulation: Anatomy and Pathology
Authors: Ritz Brianna , Nestor Nicholas , Ruiz Kristina , Aldawood Ali , Zdilla Matthew , Klinkhachorn Penprapa 
Published: March 2021

Persistent fetal lobulation of the kidneys is an uncommon condition that causes the surface of the kidney to appear as several lobules instead of smooth, flat and continuous. Persistent fetal lobulation may lead to unnecessary testing and subsequent clinical complications by masquerading as other lesions (e.g., cysts and tumors) in diagnostic imaging. Therefore, this report details the gross anatomy as well as histology of a series of lobulated kidneys. Further, this report provides gross anatomical and histological comparison with other kidney pathologies that may appear similar in diagnostic imaging.Support or Funding InformationWest Virginia University, West Liberty University, NASA West Virginia Space Grant Consortium, and West Virginia Research Challenge FundThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Novel mutations in the Myo5a gene cause a dilute coat color phenotype in mice
Authors: Zhang Hui , Wu Zhongping , Yang Lijuan , Zhang Zhen , Chen Hao , Ren Jun 
Published: March 2021

AbstractC57BL/6 laboratory mice usually show black coat color. We observed a dilute (gray) coat color phenotype in progenies of two C57BL/6 mice. This phenotype is inherited in an autosomal recessive mode. To uncover the molecular mechanism underlying this naturally occurring phenotypic variation, we performed whole‐genome sequencing (25×) on 10 offspring of the two founder mice. The whole‐genome DNA sequencing and additional RNA‐Seq data reveal that Myo5a is the gene responsible for the coat color dilution in C57BL/6 mice, and novel mutations in the Myo5a gene are likely causal. We further performed reverse transcription‐quantitative PCR, and showed increased expression of truncated Myo5a transcripts encoding dysfunctional proteins and decreased expression of Myo5a full‐length transcripts encoding functional proteins in mutant individuals. The decrease in full‐length messenger RNA abundance was accompanied by reduced Myo5a protein level and deficient melanosome transport, a potential mechanistic link between the Myo5a mutations and the dilute color phenotype. This study not only advances our understanding of the molecular mechanisms of pigmentation in mice, but also provides a typical case of deciphering the molecular basis of phenotypic variation in mice by genomic analyses and subsequent functional work.
5,6‐dihydroxy‐8Z,11Z,14Z,17Z‐eicosatetraenoic acid accelerates the healing of colitis by inhibiting transient receptor potential vanilloid 4‐mediated signaling
Authors: Kobayashi Koji , Ashina Kohei , Derouiche Sandra , Hamabata Taiki , Nakamura Tatsuro , Nagata Nanae , Takenouchi Shinya , Tominaga Makoto , Murata Takahisa 
Published: March 2021

Abstract5,6‐dihydroxy‐8Z,11Z,14Z,17Z‐eicosatetraenoic acid (5,6‐DiHETE) is an eicosapentaenoic acid‐derived lipid metabolite, which we previously detected in inflamed mouse colon. In this study, we investigated the pathophysiological roles of 5,6‐DiHETE in murine colitis and its underlying mechanisms of action, focusing on the effects on transient receptor potential vanilloid (TRPV) channel activity. Oral administration of dextran sodium sulfate (DSS, 2%, for 4 days) caused colon inflammation, which peaked on day 7 and gradually declined by day 18. 5,6‐DiHETE concentration in colon tissue was significantly increased during the healing phase of colitis (days 9 to 18). In vitro study showed that pretreatment with 5,6‐DiHETE (0.1‐1 μM, 30 minutes) significantly inhibited endothelial barrier disruption induced by a TRPV4 agonist (GSK1016790A, 50 nM). Intracellular Ca2+ imaging also showed that pretreatment with 5,6‐DiHETE (1 μM, 10 minutes) reduced GSK1016790A‐induced intracellular Ca2+ increase in HEK293T cells overexpressing TRPV4. In vivo, intraperitoneal administration of 5,6‐DiHETE (50 µg kg−1 day−1) during the healing phase accelerated the recovery from DSS‐induced colitis. Pathological studies showed that the administration of 5,6‐DiHETE inhibited edema formation and leukocyte infiltration in inflamed colon tissue. In conclusion, we identified 5,6‐DiHETE as a novel endogenous TRPV4 antagonist, and we also demonstrated that its administration promotes the healing of colitis by inhibiting inflammatory responses.
The lysosomal membrane protein Sidt2 is a vital regulator of mitochondrial quality control in skeletal muscle
Authors: Wang Lizhuo , Yu Cui , Pei Wenjun , Geng Mengya , Zhang Yao , Li Zihui , Liang Feiteng , Tan Fengbiao , Du Hui , Gao Jialin 
Published: March 2021

AbstractThe role of Sidt2 in the process of glucose and lipid metabolism has been recently reported. However, whether Sidt2 is involved in the metabolic regulation in skeletal muscle remains unknown. In this study, for the first time, using skeletal muscle‐selective Sidt2 knockout mice, we found that Sidt2 was vital for the quality control of mitochondria in mouse skeletal muscle. These mice showed significantly reduced muscle tolerance and structurally abnormal mitochondria. Deletion of the Sidt2 gene resulted in decreased expression of mitochondrial fusion protein 2 (Mfn2) and Dynamin‐related protein 1 (Drp1), as well as peroxisome proliferator‐activated receptor γ coactivator‐1 (PGC1‐α). In addition, the clearance of damaged mitochondria in skeletal muscle was inhibited upon Sidt2 deletion, which was caused by blockade of autophagy flow. Mechanistically, the fusion of autophagosomes and lysosomes was compromised in Sidt2 knockout skeletal muscle cells. In summary, the deletion of the Sidt2 gene not only interfered with the quality control of mitochondria, but also inhibited the clearance of mitochondria and caused the accumulation of a large number of damaged mitochondria, ultimately leading to the abnormal structure and function of skeletal muscle.
Polyfunctionality of the CXCR4/CXCL12 axis in health and disease: Implications for therapeutic interventions in cancer and immune‐mediated diseases
Authors: Britton C. , Poznansky M. C. , Reeves P. 
Published: March 2021

AbstractHistorically the chemokine receptor CXCR4 and its canonical ligand CXCL12 are associated with the bone marrow niche and hematopoiesis. However, CXCL12 exhibits broad tissue expression including brain, thymus, heart, lung, liver, kidney, spleen, and bone marrow. CXCR4 can be considered as a node which is integrating and transducing inputs from a range of ligand‐receptor interactions into a responsive and divergent network of intracellular signaling pathways that impact multiple cellular processes such as proliferation, migration, and stress resistance. Dysregulation of the CXCR4/CXCL12 axis and consequent fundamental cellular processes, are associated with a panoply of disease. This review frames the polyfunctionality of the receptor at a molecular, physiological, and pathophysiological levels. Transitioning our perspective of this axis from a single gene/protein:single function model to a polyfunctional signaling cascade highlights the potential for finer therapeutic intervention and cautions against a reductionist approach.