bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance
Authors: Stanford Kim , Tran Frances , Zhang Peipei , Yang Xianqin 
Published: March 2021

AbstractDespite the importance of biofilm formation in contamination of meat by pathogenic Escherichia coli at slaughter plants, drivers for biofilm have been unclear. To identify selection pressures for biofilm, we evaluated 745 ‘Top 7’ from cattle and 700 generic E. coli from two beef slaughter plants for motility, expression of curli and cellulose, and biofilm-forming potential. Top 7 were also screened for serogroup, stx1, stx2, eae and rpoS. Generic E. coli were compared by source (hide of carcass, hide-off carcass, processing equipment) before and after implementation of antimicrobial hurdles. The proportion of E. coli capable of forming biofilms was lowest (7.1%; P < 0.05) for cattle isolates and highest (87.3%; P < 0.05) from equipment. Only one enterohemorrhagic E. coli (EHEC) was an extremely-strong biofilm-former, in contrast to 73.4% of E. coli from equipment. Isolates from equipment after sanitation had a greater biofilm-forming capacity (P < 0.001) than those before sanitation. Most Top 7 were motile and expressed curli, although these traits along with expression of cellulose and presence of rpoS were not necessary for biofilm formation. In contrast, isolates capable of forming biofilms on equipment were almost exclusively motile and able to express curli. Results of the present study indicate that cattle would rarely carry EHEC capable of making strong biofilms to slaughter plants. However, if biofilm-forming EHEC contaminated equipment, current antimicrobial hurdles would inadvertently perpetuate the most robust biofilm-forming strains. Accordingly, new and effective anti-biofilm hurdles are required for meat-processing equipment, to reduce future instances of food-borne disease.ImportanceAs the majority of enterohemorrhagic E. coli (EHEC) are not capable of forming biofilms, sources were undetermined of the biofilm-forming EHEC isolated from ‘high-event periods’ in beef slaughter plants. This study demonstrated that sanitation procedures used on beef-processing equipment inadvertently select for survival of the most robust biofilm-forming strains of E. coli. Cattle only rarely carry EHEC capable of forming strong biofilms (1/745 isolates evaluated), but sanitation of equipment markedly increased (P < 0.001) biofilm-forming capacity of E. coli. In contrast, chilling carcasses for 3 days at 0°C reduced (P < 0.05) biofilm-forming capacity of E. coli. Consequently, an additional anti-biofilm hurdle for meat-processing equipment, perhaps involving cold exposure, is necessary to further reduce the risk of food-borne disease.
Neural circuitry for maternal oxytocin release induced by infant cries
Authors: Valtcheva Silvana , Issa Habon A. , Bair-Marshall Chloe J. , Martin Kathleen A. , Jung Kanghoon , Zhang Yiyao , Kwon Hyung-Bae , Froemke Robert C. 
Published: March 2021

AbstractOxytocin is a neuropeptide important for maternal physiology and childcare, including parturition and milk ejection during nursing1–8. Suckling triggers oxytocin release, but other sensory cues- specifically infant cries- can elevate oxytocin levels in new human mothers9–11indicating that cries can activate hypothalamic oxytocin neurons. Here we describe a neural circuit routing auditory information about infant vocalizations to mouse oxytocin neurons. We performed in vivo electrophysiological recordings and photometry from identified oxytocin neurons in awake maternal mice presented with pup calls. We found that oxytocin neurons responded to pup vocalizations, but not pure tones, via input from the posterior intralaminar thalamus, and repetitive thalamic stimulation induced lasting disinhibition of oxytocin neurons. This circuit gates central oxytocin release and maternal behavior in response to calls, providing a mechanism for the integration of sensory cues from the offspring in maternal endocrine networks to ensure modulation of brain state for efficient parenting.
Identifying Brain Regions Related to Word Prediction During Listening to Japanese Speech by Combining a LSTM Language Model and MEG
Authors: Takahashi Yuta , Oseki Yohei , Sakai Hiromu , Makuuchi Michiru , Osu Rieko 
Published: March 2021

AbstractRecently, a neuroscientific approach has revealed that humans understand language while subconsciously predicting the next word from the preceding context. Most studies on human word prediction have investigated the correlations between brain activity while reading or listening to sentences on functional magnetic resonance imaging (fMRI) and the predictive difficulty of each word in a sentence calculated by the N-gram language model. However, because of its low temporal resolution, fMRI is not optimal for identifying the changes in brain activity that accompany language comprehension. In addition, the N-gram language model is a simple computational structure that does not account for the structure of the human brain. Furthermore, it is necessary for humans to retain information prior to the N-1 word in order to form a contextual understanding of a presented story. Therefore, in the present study, we measured brain activity using magnetoencephalography (MEG), which has a higher temporal resolution than fMRI, and calculated the prediction difficulty of words using a long short-term memory language model (LSTMLM), which is based on a neural network inspired by the structure of the human brain and has longer information retention than the N-gram language model. We then identified the brain regions involved in language prediction during Japanese-language speech listening using encoding and decoding analyses. In addition to surprisal-related regions revealed in previous studies, such as the superior temporal gyrus, fusiform gyrus, and temporal pole, we also found relationships between surprisal and brain activity in other regions, including the insula, superior temporal sulcus, and middle temporal gyrus, which are believed to be involved in longer-term, sentence-level cognitive processing.
Effect of temperature and loading frequency on the performance of vertical subsurface flow constructed wetlands: Modelling study using HYDRUS
Authors: Jayswal Nikita , Rodríguez Jorge 
Published: March 2021

AbstractConstructed wetlands are used in wastewater treatment for the removal of organic matter, nutrients, pathogens and other pollutants from water. The diversity of chemical, physical and biological processes taking place inside constructed wetlands (CWs) make them difficult systems for accurate quantitative description through conventional modelling approaches. However, existing modelling tools can bring valuable insight into important phenomena and interactions that might remain otherwise neglected. In this study the CW2D module under HYDRUS – 2D is used to identify the possible mechanisms by which temperature and loading frequency impacts the performance of the vertical subsurface flow constructed wetlands (VSSFCWs). An improvement on CWs design and operation guidelines in warm regions is intended. Case studies of a VSSFCW at 10°C, 20°C and 30°C treating septic tank effluent are simulated with parameters adjusted for high temperature conditions. The simulation results suggest oxygen limitation as possibly constraining nitrification capacity at high temperatures. Simulations also suggest that higher loading frequencies enhance performance and capacity. This detailed mechanistic modelling study aims at bringing insight into possible non trivial interactions and mechanisms in CWs such that in conjunction with a necessary experimental validation, should lead to enhanced operation and design in warm regions.
The Nestin neural enhancer is essential for normal levels of endogenous Nestin in neuroprogenitors but is not required for embryo development
Authors: Thomson Ella , Dawson Ruby , H’ng Chee Ho , Adikusuma Fatwa , Piltz Sandra , Thomas Paul Q 
Published: March 2021

AbstractEnhancers are vitally important during embryonic development to control the spatial and temporal expression of genes. Recently, large scale genome projects have identified a vast number of putative developmental regulatory elements. However, the proportion of these that have been functionally assessed is relatively low. While enhancers have traditionally been studied using reporter assays, this approach does not characterise their contribution to endogenous gene expression. We have studied the murine Nestin (Nes)intron 2 enhancer, which is widely used to direct exogenous gene expression within neural progenitor cells in cultured cells andin vivo. We generated CRISPR deletions of the enhancer region in mice and assessed their impact onNesexpression during embryonic development. Loss of theNesneural enhancer significantly reducedNesexpression in the developing CNS by as much as 82%. By assessing NES protein localization, we also show that this enhancer region contains repressor element(s) that inhibitNesexpression within the vasculature. Previous reports have stated thatNesis an essential gene, and its loss causes embryonic lethality. We also generated 2 independentNesnull lines and show that both develop without any obvious phenotypic effects. Finally, through crossing of null and enhancer deletion mice we provide evidence oftrans-chromosomal interaction of theNesenhancer and promoter.
Astrocytes render memory flexible
Authors: Koh Wuhyun , Park Mijeong , Chun Ye Eun , Lee Jaekwang , Shim Hyun Soo , Park Mingu Gordon , Kim Sunpil , Kang Hyunji , Oh Soo-Jin , Woo Junsung , Chun Heejung , Lee Seungeun , Hong Jinpyo , Feng Jiesi , Li Yulong , Ryu Hoon , Cho Jeiwon , Lee C. Justin 
Published: March 2021

SummaryCognitive flexibility is an essential ability to adapt to changing environment and circumstances. NMDAR has long been implicated in cognitive flexibility, but the precise molecular and cellular mechanism is not well understood. Here, we report that astrocytes regulate NMDAR tone through Best1-mediated glutamate and D-serine release, which is critical for cognitive flexibility. Co-release of D-serine and glutamate is required for not only homosynaptic LTD but also heterosynaptic LTD, which is induced at unstimulated synapses upon release of norepinephrine and activation of astrocytic α1-AR during homosynaptic LTP. Remarkably, heterosynaptic LTD at unstimulated synapses during memory acquisition is required for later repotentiation LTP during reversal learning, laying a foundation for flexible memory and cognitive flexibility. Our study sheds light on the pivotal role of astrocytes in orchestrating multiple synapses during memory formation and determining the fate of consolidated memory to be retained as a flexible memory.HighlightsAstrocytes regulate NMDAR tone via Best1-mediated glutamate and D-serine releaseActivation of astrocytic α1-AR induces heterosynaptic LTD via NMDAR toneHeterosynaptic LTD is required for repotentiation LTP and spatial reversal learningAstrocytic regulation of NMDAR tone is critical for metaplasticity and flexible memory
Spatiotemporal patterns in Golden-cheeked Warbler breeding habitat quality and quantity
Authors: Dreiss Lindsay M. , Sanchez-Navarro Paul , Bird Bryan 
Published: March 2021

ABSTRACTThe Golden-cheeked Warbler,Setophaga chrysoparia, is a migratory songbird listed as endangered under the federal Endangered Species Act that breeds exclusively in central Texas and is heavily impacted by habitat conversion. The species relies on mixed Ashe-juniper and oak woodlands for nest-building and shelter during spring and early summer months. Using land cover data spanning the last 25 years, we conduct a geospatial analysis to quantify changes and\ identify shifts in breeding habitat quantity and quality. Since 1985, 13% of all forests within the warbler’s breeding range were disturbed, with greater incidences near San Antonio (32%) and Austin (24%) metropolitan areas. Additionally, data show a 45% decrease in high-quality habitat (i.e., intact mixed or evergreen core forests) and a decrease in patch size. Habitats within protected areas see a less sharp decline in habitat quality and large increases in warbler sightings, but these only represent 10% of all highest-quality habitat in the breeding range. Drastic declines in habitat quality suggest that generalized metrics of conversion may underestimate true habitat loss as degradation may impact the ecological viability of remaining forests for warbler nesting. Further evidence suggests that the few protected areas within the Texas range continue to play a significant role in warbler breeding. This information will assist researchers and managers prioritizing conservation action and will inform upcoming species status determinations.
Unsupervised temporal consistency improvement for microscopy video segmentation with Siamese networks
Authors: Shabanov Akhmedkhan , Schichler Daja , Pape Constantin , Cuylen-Haering Sara , Kreshuk Anna 
Published: March 2021

ABSTRACTWe introduce a simple mechanism by which a CNN trained to perform semantic segmentation of individual images can be re-trained - with no additional annotations - to improve its performance for segmentation of videos. We put the segmentation CNN in a Siamese setup with shared weights and train both for segmentation accuracy on annotated images and for segmentation similarity on unlabelled consecutive video frames. Our main application is live microscopy imaging of membrane-less organelles where the fluorescent groundtruth for virtual staining can only be acquired for individual frames. The method is directly applicable to other microscopy modalities, as we demonstrate by experiments on the Cell Segmentation Benchmark. Our code is available athttps://github.com/kreshuklab/learning-temporal-consistency.
The influence of sex, hormone status, and growth rate on dietary isotope fractionation: a case study with laboratory rats
Authors: Kim Sora L. , Jones Caroline , Santollo Jessica 
Published: March 2021

ABSTRACTStable isotope analysis is increasingly used to discern ecological differences within and among species, especially those difficult to observe. In applied ecological studies, variations in stable isotope composition are often attributed to foraging behavior or trophic ecology rather than fractionation during metabolic processes. One physiological difference among individuals is gonadal hormone levels, which affects food intake, metabolism, and locomotor activity. However, it is unclear how these effects– isolated from ecology– affect metabolic dynamics and expression in stable isotope analysis. Here, we test the linkage between gonadal hormones and isotopic heterogeneity among individuals with captive rats. We found that sex and removal of gonadal hormones are factors either individually or interactive for δ15N and δ13C values in serum and blood as well as δ15N values of muscle and liver. Furthermore, the degree of fractionation in these tissues is related to growth rate. Gonadectomization also affected isotopic composition for liver δ13C values and kidney δ15N values, but fat δ13C values were affected only by sex. The pattern of differentiation between groups was most different for kidney δ15N and δ13C values, which also had the largest isotopic variability among groups. Overall, isotopic variation within one tissue for the four groups demonstrated up to 1‰ difference in δ13C and δ15N values suggesting that sex based within population variations should into consideration these potential physiological effects.What is already knownThere are isotopic differences between diet and various consumer tissues with variability among individuals, which is often characterized based on captive feeding studies. Effects of protein quality and quantity, variable growth rate based on ontogeny, and differences between sexes have been tested thus far in experiments. Furthermore, it is known that gonadal hormones affect energy regulation with difference in weight gain, which suggest differences in extent and rate of biochemical processes.What this study addsThis study demonstrates effects of gonadal hormone status with metabolic biochemistry by using stable isotopes of carbon and nitrogen as dietary tracers. We find that gonadal hormone status accounts for some isotopic heterogeneity among individuals, which should be considered when interpreting stable isotope data from wild specimens. Rather than attributing isotopic differences to ecological factors, such as foraging preference, there may be underlying physiological processes that differentiate groups based on ontogeny and sex.
Gene Conversion Facilitates the Adaptive Evolution of Self-Resistance in Highly Toxic Newts
Authors: Gendreau Kerry L. , Hornsby Angela D. , Hague Michael T. J. , McGlothlin Joel W. 
Published: March 2021

AbstractReconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology.Tarichanewts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Nav) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance by sequencing the entire Navgene family in newts and related salamanders. We show that moderate TTX resistance evolved early in the salamander lineage in three of the six Navparalogs, preceding the proposed appearance of tetrodotoxic newts by ∼100 million years. TTX-bearing newts possess additional unique substitutions across the entire Navgene family that provide physiological TTX resistance. These substitutions coincide with signatures of positive selection and relaxed purifying selection, as well as gene conversion events, that together likely facilitated their evolution. We also identify a novel exon duplication within Nav1.4 encoding an expressed TTX-binding site. Two resistance-conferring changes within newts appear to have spread via nonallelic gene conversion: in one case, one codon was copied between paralogs, and in the second, multiple substitutions were homogenized between the duplicate exons of Nav1.4. Our results demonstrate that gene conversion can accelerate the coordinated evolution of gene families in response to a common selection pressure.
Higher-order interactions among coinfecting parasites and a microbial mutualist impact disease progression
Authors: O’Keeffe Kayleigh R. , Simha Anita , Mitchell Charles E. 
Published: March 2021

AbstractInteractions among parasites and other microbes within hosts can impact disease progression, yet study of such interactions has been mostly limited to pairwise combinations of microbes. Given the diversity of microbes within hosts, higher-order interactions among more than two microbial species may also impact disease. To test this hypothesis, we performed inoculation experiments that investigated interactions among two fungal parasites,Rhizoctonia solaniandColletotrichum cereale, and a systemic fungal endophyte,Epichloë coenophiala, within a grass host. Both pairwise and higher-order interactions impacted disease progression. While the endophyte did not directly influenceR. solanigrowth orC. cerealesymptom development, the endophyte modified the interaction between the two parasites. The magnitude of the facilitative effect ofC. cerealeon the growth ofR. solanitended to be greater when the endophyte was present. Moreover, this interaction modification strongly affected leaf mortality. For plants lacking the endophyte, parasite co-inoculation did not increase leaf mortality compared to single-parasite inoculations. In contrast, for endophyte-infected plants, parasite co-inoculation increased leaf mortality compared to inoculation withR. solaniorC. cerealealone by 1.9 or 4.9 times, respectively. Together, these results show that disease progression can be strongly impacted by higher-order interactions among microbial symbionts.
Differential effects of loss ofpark7activity on Iron Responsive Element (IRE) gene sets: Implications for the role of iron dyshomeostasis in the pathophysiology of Parkinson’s disease
Authors: Chin Hui Yung , Lardelli Michael , Collins-Praino Lyndsey , Barthelson Karissa 
Published: March 2021

AbstractMutation of the genePARK7(DJ1) causes monogenic autosomal recessive Parkinson’s disease (PD) in humans. Subsequent alterations of PARK7 protein function lead to mitochondrial dysfunction, a major element in PD pathology. Homozygous mutants for thePARK7-orthologous genes in zebrafish,park7, show changes to gene expression in the oxidative phosphorylation pathway, supporting that disruption of energy production is a key feature of neurodegeneration in PD. Iron is critical for normal mitochondrial function, and we have previously used bioinformatic analysis of IRE-bearing transcripts in brain transcriptomes to find evidence supporting the existence of iron dyshomeostasis in Alzheimer’s disease. Here, we analysed IRE-bearing transcripts in the transcriptome data from homozygouspark7−/−mutant zebrafish brains. We found that the set of genes with “high quality” IREs in their 5’ untranslated regions (UTRs, the HQ5’IRE gene set) was significantly altered in these 4-month-oldpark7−/−brains. However, sets of genes with IREs in their 3’ UTRs appeared unaffected. The effects on HQ5’IRE genes are possibly driven by iron dyshomeostasis and/or oxidative stress, but illuminate the existence of currently unknown mechanisms with differential overall effects on 5’ and 3’ IREs.
Sex disparities in influenza: a multiscale network analysis
Authors: Wang Chang , Lashua Lauren P. , Carter Chalise E. , Johnson Scott K. , Wang Minghui , Ross Ted M. , Ghedin Elodie , Zhang Bin , Forst Christian V. 
Published: March 2021

SUMMARYSex differences in the pathogenesis of infectious diseases due to differential immune responses between females and males have been well documented for multiple pathogens. However, the molecular mechanism underlying the observed sex differences in influenza virus infection remains poorly understood. In this study, we used a network-based approach to characterize the blood transcriptome collected over the course of infection with influenza A virus from female and male ferrets to dissect sex-biased gene expression. We identified significant differences in the temporal dynamics and regulation of immune responses between females and males. Our results elucidate sex-differentiated pathways involved in the unfolded protein response (UPR), lipid metabolism, and inflammatory responses, including a female-biased IRE1/XBP1 activation and male-biased crosstalk between metabolic reprogramming and IL-1 and AP-1 pathways. Overall, our study provides molecular insights into sex differences in transcriptional regulation of immune responses and contributes to a better understanding of sex bias in influenza pathogenesis.