bluuebunny/crossref_metadata_2025_split huggingface dataset:
The concentration of tuberculosis within Paraguay’s incarcerated and Indigenous populations, 2018-2022
Authors: Medina Angélica , Sussman Jacob , Sosa Natalia , Valdez Melissa , Andrews Jason R. , Croda Julio , Sanabria Gladys Estigarribia , Sequera Guillermo , Aguirre Sarita , Walter Katharine S. 
Published: June 2024

AbstractWhile incidence of tuberculosis (TB) has decreased globally, in Paraguay, considered a medium-incidence country by the WHO, TB incidence has increased slightly from 42 per 100,000 in 2010 to 46 per 100,000 in 2022. We conducted a retrospective study of TB cases notified to the Paraguay National Program for Tuberculosis Control (NPTC) from 2018 to 2022 and quantified trends in specific populations identified as vulnerable. Of the 13,725 TB cases notified in Paraguay from 2018 to 2022, 2,331 (17%) occurred among incarcerated individuals and 1,743 (12.7%) occurred among self-identified Indigenous individuals. In 2022, the relative risk of TB was 87 and 6.4 among the incarcerated and Indigenous populations, compared with the non-incarcerated and non-Indigenous populations respectively. We found significant heterogeneity in TB incidence across Paraguay’s 17 departments. Our findings highlight the urgency of expanding access to TB diagnosis, treatment, and prevention in populations at heightened risk of TB in Paraguay.
ACUTE KIDNEY INJURY AS A PREDICTOR OF IN-HOSPITAL MORTALITY IN PATIENTS WITH A DIAGNOSIS OF SEVERE COVID-19
Authors: Ordinola Anthonela Cruz , Arriola Carlos Fajardo , Ato Raúl Sandoval 
Published: June 2024

SUMMARYOBJECTIVEDetermine if Acute Kidney Injury (AKI) is a predictor of In-hospital Mortality in severe Covid-19 patients.METHODSA retrospective cohort study was carried out with severe Covid-19 patients from the Hospital de la Amistad Perú - Corea Santa Rosa II - Piura, using a multivariate analysis with the bivariate logistic regression technique and the method = Advance by steps (ratio of likelihood), to calculate a predictive model for Mortality in Covid-19 patients exposed to ARI.RESULTSMortality was higher in the cohort exposed to ARI (95% vs 71.9%) and a 5-fold RR of death in the patient exposed to ARI compared to the Covid-19 patient not exposed to ARI.CONCLUSIONExposure to ARI increases the risk of mortality by 5 times, increasing the risk of mortality based on the increase in the SOFA score upon admission to the ICU and increase in mg/dl of C-Reactive Protein.
Surgical Decision-Making in Neonates with Borderline Left Ventricular Hypoplasia without Significant Aortic or Mitral Valve Stenosis using Cardiovascular Magnetic Resonance
Authors: House Aswathy Vaikom , Singh Aakansha , Sapruangrang Ankavipar , Jaeggi Edgar , Barron David J. , Lam Christopher Z. , Yoo Shi-Joon 
Published: June 2024

AbstractBackgroundMost patients with significant left ventricular (LV) hypoplasia undergo single ventricle (SV) palliation, but biventricular (Bi-V) repair is viable in some patients with borderline LV hypoplasia. We sought to identify CMR (cardiovascular magnetic resonance) criteria predictive of successful primary Bi-V repair in neonates with borderline LV hypoplasia without significant stenosis of the mitral valve (MV) and aortic valve (AV), and to determine reasons for reintervention after successful Bi-V repair.MethodsThis retrospective study included all patients with borderline LV hypoplasia who underwent CMR from 2003-2024 for surgical decision-making. Patients with abnormal segmental connections, atrioventricular septal defects, unrestrictive ventricular septal defects, those with more than mild MV stenosis (mean Doppler flow gradient > 5 mmHg) and/or more than mild AV stenosis (peak Doppler flow gradient >20 mmHg) were excluded. Patients were divided into two groups based on initial intervention - primary Bi-V repair and hybrid/ other staging procedure. Outcomes were categorized as successful primary Bi-V repair, successful staged Bi-V repair and failure to achieve Bi-V repair (hybrid followed by SV palliation, transplant, death). Fisher exact test and Mann-Whitney U test was utilized to explore potential relationships. ROC curves were used to test diagnostic accuracy of parameters to predict successful primary Bi-V repair.ResultsAmong 37 patients meeting the inclusion criteria, 23 (62%) patients underwent successful primary Bi-V repair, 8 (22%) underwent staged Bi-V repair, 6 (16%) failed to achieve Bi-V repair. Patients who underwent successful primary/ staged Bi-V repair had higher values for left ventricular diastolic volume index (LVEDVi 28 mL/m2vs. 17.4.00 mL/m2; p <0.002), higher blood flow volume through the ascending aorta (QAo:1.99 L/min/m2vs. 0.97 L/min/m2, p <0.012), and QAo/ superior vena cava (QSVC) flow ratio (1.44 vs. 0.85, p =0.034) compared to those who had failure to achieve Bi-V repair. CMR LVEDVi cutoff of CMR 27 mL/m², had 87% sensitivity and 79% specificity with an AUC of 87.6% and QAothreshold of 1.9 L/min/m2had 65.2% sensitivity and 92.9% specificity (AUC: 86.0%) to predict successful primary Bi-V repair. Of 31 patients with primary or staged Bi-V repair, 7 (22%) underwent reinterventions for LVOT obstruction followed by mitral stenosis.ConclusionsCMR plays a critical role in pre-operative evaluation, surveillance and decision-making in patients with borderline LV hypoplasia. In patients with borderline LV hypoplasia without MV/AV stenosis, successful primary Bi-V repair can be achieved when the CMR-derived LVEDVi is >27 mL/m2and QAois > 1.99 L/min/m2.
Direct observation of fluorescent proteins in gels: a rapid cost-efficient, and quantitative alternative to immunoblotting
Authors: Sanial Matthieu , Miled Ryan , Alves Marine , Claret Sandra , Joly Nicolas , Proux-Gillardeaux Véronique , Plessis Anne , Léon Sébastien 
Published: June 2024

AbstractThe discovery of Green Fluorescent Protein (GFP) and its derivatives has revolutionized cell biology. These fluorescent proteins (FPs) have enabled the real-time observation of protein localization and dynamics within live cells. Applications of FP vary from monitoring gene/protein expression patterns, visualizing protein-protein interactions, measuring protein stability, assessing protein mobility and creating biosensors. The utility of FPs also extends to biochemical approaches through immunoblotting and proteomic analyses, aided by anti-FP antibodies and nanobodies. FPs are notoriously robust proteins with a tightly folded domain that confers a strong stability and a relative resistance to degradation and denaturation. In this study, we report that various green, orange and red FPs can be maintained in a native, fluorescent state during the entire process of protein sample extraction, incubation with sample buffer, loading and migration on SDS-PAGE with only minor adaptations of traditional protocols. This protocol results in the ability to detect and quantify in-gel fluorescence (IGF) of endogenously-expressed proteins tagged with FPs directly after migration, using standard fluorescence-imaging devices. This approach eliminates the need for antibodies and chemiluminescent reagents, as well as the time-consuming steps inherent in immunoblotting such as transfer onto a membrane and antibody incubations. Overall, IGF detection provides clearer data with less background interference, a sensitivity comparable or better to antibody-based detection, a better quantification and a broader dynamic range. After fluorescence imaging, gels can still be used for other applications such as total protein staining or immunoblotting if needed. It also expands possibilities by allowing the detection of FPs for which antibodies are not available. Our study explores the feasibility, limitations, and applications of IGF for detecting endogenously expressed proteins in cell extracts, providing insights into sample preparation, imaging conditions, and sensitivity optimizations, and potential applications such as co-immunoprecipitation experiments.
Robust encoding of acoustic identity in alpaca hums - a basis for individual recognition
Authors: Wierucka Kaja , Leu Stephan T. 
Published: June 2024

ABSTRACTIndividual recognition is an important element of social interactions among animals. While the presence of individually distinct vocalisations (providing a basis for individual recognition) has been widely tested across species, information about which components of a call encode this information is lacking. We investigated whether female alpaca (Vicugna pacos) vocalisations, particularly their hums, encode information about individual identity and explored which parameters contribute to this encoding. We recorded vocalisations from 9 adult female alpaca and extracted both spectro-temporal features (frequencies and duration) and mel-frequency cepstral coefficients (MFCC). Random forest analyses revealed clear individual differences in both datasets, with the spectro-temporal features allowing for slightly more accurate classification than MFCC (71% and 66.5% accuracy for spectro-temporal features and MFCC, respectively). These robust acoustic identities have the potential to provide a basis for individual recognition in alpaca, which could have important flow on effects for alpaca communication, as it allows receivers to modulate their response to the caller’s identity. Alpaca, as herd-living and vocal animals, provide an excellent model system for better understanding the mechanisms, causes and consequences of recognition and inter-individual communication.
Vaccine strains of Rift Valley fever virus exhibit attenuation at the maternal-fetal placental interface
Authors: McMillen Cynthia M. , Megli Christina , Radisic Rebecca , Skvarca Lauren B. , Hoehl Ryan M. , Boyles Devin A. , McGaughey Jackson J. , Bird Brian H. , McElroy Anita K. , Hartman Amy L. 
Published: June 2024

AbstractRift Valley fever virus (RVFV) infection causes abortions in ruminant livestock and is associated with an increased likelihood of miscarriages in women. Using sheep and human placenta explant cultures, we sought to identify tissues at the maternal-fetal interface targeted by RVFV. Sheep villi and fetal membranes were highly permissive to RVFV infection resulting in markedly higher virus titers than human cultures. Sheep cultures were most permissive to wild-type RVFV and ΔNSm infection, while live attenuated RVFV vaccines (LAVs; MP-12, ΔNSs, and ΔNSs/ΔNSm) exhibited reduced replication. The human fetal membrane restricted wild-type and LAV replication, and when infection occurred, it was prominent in the maternal-facing side. Type-I and type-III interferons were induced in human villi exposed to LAVs lacking the NSs protein. This study supports the use of sheep and human placenta explants to understand vertical transmission of RVFV in mammals and whether LAVs are attenuated at the maternal-fetal interface.TeaserVaccine strains of Rift Valley fever virus have reduced infection and replication capacity in mammalian placenta
Systems genomics of salinity stress response in rice
Authors: Gupta Sonal , Groen Simon C. , Zaidem Maricris L. , Sajise Andres Godwin C. , Calic Irina , Natividad Mignon A. , McNally Kenneth L. , Vergara Georgina V. , Satija Rahul , Franks Steven J. , Singh Rakesh K. , Joly-Lopez Zoé , Purugganan Michael D. 
Published: June 2024

ABSTRACTPopulations can adapt to stressful environments through changes in gene expression. However, the fitness effect of gene expression in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants ofOryza sativassp. indica(rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show thattrans-eQTLs rather thancis-eQTLs are primarily associated with rice’s gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find thatcis-transreinforcement is more common thancis-transcompensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show thatcis- andtrans-eQTLs are under balancing and purifying selection, respectively, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.
LC-SRM combined with machine learning enables fast identification and quantification of bacterial pathogens in urinary tract infections
Authors: Gotti Clarisse , Roux-Dalvai Florence , Bérubé Ève , Lacombe-Rastoll Antoine , Leclercq Mickaël , Jacob Cristina C. , Boissinot Maurice , Martins Claudia , Wijeratne Neloni R. , Bergeron Michel G. , Droit Arnaud 
Published: June 2024

ABSTRACTUrinary tract infections (UTIs) are a worldwide health problem. Fast and accurate detection of bacterial infection is essential to provide appropriate antibiotherapy to patients and to avoid the emergence of drug-resistant pathogens. While the gold standard requires 24h to 48h of bacteria culture prior MALDI-TOF species identification, we propose a culture-free workflow, enabling a bacterial identification and quantification in less than 4 hours using 1mL of urine. After a rapid and automatable sample preparation, a signature of 82 bacterial peptides, defined by machine learning, was monitored in LC-MS, to distinguish the 15 species causing 84% of the UTIs. The combination of the sensitivity of the SRM mode on a triple quadrupole TSQ Altis instrument and the robustness of capillary flow enabled us to analyze up to 75 samples per day, with 99.2% accuracy on bacterial inoculations of healthy urines. We have also shown our method can be used to quantify the spread of the infection, from 8×104to 3×107CFU/mL. Finally, the workflow was validated on 45 inoculated urines and on 84 UTI-positive urine from patients, with respectively 93.3% and 87.1% of agreement with the culture-MALDI procedure at a level above 1×105CFU/mL corresponding to an infection requiring antibiotherapy.HIGHLIGHTS– LC-MS-SRM and machine learning to identify and quantify bacterial species of UTI– Fast sample preparation without bacterial culture and high-throughput MS analysis– Accurate quantification through calibration curves for 15 species of UTIs– Validation on inoculations (93% accuracy) and on patients specimens (87% accuracy)
Estrous phase during fear extinction modulates fear relapse through a nigrostriatal dopamine pathway
Authors: Hohorst Alyssa A , Tanner Margaret K , Han Rebecca , Korth Kamryn , Westerman Jessica D , Mendoza Carolina Sanchez , Dryden Miles Q , Alverez Lareina , Abdul Remla , Loetz Esteban C , Oleson Erik B , Greenwood Benjamin N 
Published: June 2024

AbstractElevated ovarian hormones during fear extinction can enhance fear extinction memory retention and reduce renewal, but the mechanisms remain unknown. Ovarian hormones modulate dopamine (DA) transmission, a key player in fear extinction. In males, stimulation of substantia nigra (SN) DA neurons during fear extinction reduces renewal; an effect mimicked by a DA D1 receptor agonist into the dorsolateral striatum (DLS). The current studies tested the role of the SN-DLS pathway in estrous cycle-modulation of fear extinction and relapse. In cycling female, Long-Evans rats, fear extinction during proestrus or estrus (Pro/Est; high hormones) resulted in less relapse (renewal and spontaneous recovery) compared to males or females in metestrus or diestrus (Met/Di; low hormones). This effect was mimicked by estradiol (E2) administration to ovariectomized rats. Females in Pro/Est had greater fear extinction-induced cFos within SN DA neurons compared to males. Similarly, fast scan cyclic voltammetry revealed that electrically-evoked DA release in the DLS is potentiated by E2 and is greater during Pro/Est compared to Met/Di. An inhibitory intersectional chemogenetic approach targeting the SN-DLS pathway suppressed electrically-evoked DA release in the DLS and restored fear renewal in females exposed to simultaneous fear extinction and SN-DLS inhibition during Pro/Est. Conversely, chemogenetic stimulation of the SN-DLS pathway during extinction reduced fear renewal in males. These data suggest that levels of ovarian hormones present during fear extinction modulate relapse through a SN-DLS pathway, and that the SN-DLS pathway represents a novel target for the reduction of fear relapse in both sexes.
The double-edged sword of urban life: Invasive grey squirrels perceive foraging as safer close to roads under noisier conditions, yet riskier when noise is inconsistent
Authors: Thompson Kristin P. J. , Dall Sasha R.X. 
Published: June 2024

AbstractMortality risk influences decisions of foraging animals such that foraging and feeding behaviours are usually biased towards habitats where benefits of feeding outweigh risks. Human activity and associated disturbance are thought to be perceived as a source of risk analogous to predation risk in wildlife. As such, can alter behaviour and habitat use of foraging animals.Urban wildlife faces increased exposure to human disturbance, meaning that they may face an increase in perceived risk during food acquisition. Urban habitats also include novel and altered food resources that could result in urban wildlife having to face distinct trade-offs associated with foraging and patch use compared to rural counterparts.To examine how a relatively successful invasive urban mammal, the eastern grey squirrel, balances risk and safety under human disturbance, we measured giving-up densities (GUD) at artificial food patches placed at sites subject to varying levels of urbanisation to investigate how features associated with human disturbance might influence feeding decisions.We found that differences in GUDs between ‘safe’ and risky’ patches were reduced closer to roads only under noisy conditions, suggesting that the risk of predation is perceived by squirrels as reduced when disturbance from human activities is highest. However, there was also a significant effect of the variability in noise levels on patterns of patch exploitation, with higher GUDs and larger GUD differences between safe and risky patches found under more variable noise levels, suggesting that squirrels might also find dynamic human disturbances startling or distracting while foraging.Synthesis: Our results show how human activities can have doubled-edged impacts on the urban landscape of fear through offering reduced risk from predators whilst increasing foraging costs via noise disturbance. Future research could consider how foraging decisions in urban wildlife vary according to food supply and disturbance levels, to shed further light on foraging trade-offs made by wildlife under increasing urbanisation levels.
Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage
Authors: Loh Ling S. , DeMarr Kyle A. , Tsimba Martina , Heryanto Christa , Berrio Alejandro , Patel Nipam H. , Martin Arnaud , McMillan W. Owen , Wray Gregory A. , Hanly Joseph J. 
Published: June 2024

AbstractThe success of butterflies and moths is tightly linked to the origin of scales within the group. A long-standing hypothesis postulates that scales are homologous to the well-described mechanosensory bristles found in the fruit flyDrosophila melanogaster, where both derive from an epithelial precursor specified by lateral inhibition that then undergoes multiple rounds of division. Previous histological examination and candidate gene approaches identified parallels in genes involved in scale and bristle development. Here, we provide definitive developmental and transcriptomic evidence that the differentiation of lepidopteran scales derives from the canonical cell lineage, known as the Sensory Organ Precursor (SOP). Live imaging in moth and butterfly pupae shows that SOP cells undergo two rounds of asymmetric divisions that first abrogate the neurogenic lineage, and then lead to a differentiated scale precursor and its associated socket cell. Single-nucleus RNA sequencing across a time-series of early pupal development revealed differential gene expression patterns that mirror canonical lineage development, including Notch-Delta signalling components, cell adhesion molecules, cell cycling factors, and terminal cell differentiation markers, suggesting a shared origin of the SOP developmental program. Additionally, we recovered a novel gene, the POU-domain transcription factorpdm3, involved in the proper differentiation of butterfly wing scales. Altogether, these data open up avenues for understanding scale type specification and development, and illustrate how single-cell transcriptomics provide a powerful platform for understanding the evolution of cell types.
Some like it hot: efficiency of the type III secretion system and activation of plant defenses have multiple thermosensitive behaviors in thePseudomonas syringaecomplex
Authors: Caullireau E. , Danzi D. , Tempo V.M. , Pandolfo M. , Morris C.E. , Vandelle E. 
Published: June 2024

AbstractThePseudomonas syringaespecies complex is a very important plant pathogenic bacterium, causing damage and economic losses on many crops. Research efforts for the understanding of the determinants of the host-range of a given strain are considerable. Recently, we showed that the inability of aP. syringaepv.actinidiaestrain to trigger ETI inA. thalianais due to an inefficient T3SS and not to the absence of a recognized effector. In this context, we compared severalP. syringaestrains belonging to different phylogroups and carrying the same plasmid-born avirulence gene for their ability to induce an HR inA. thalianaCol-0, as a marker of T3SS efficiency.PtoDC3000AvrBandPmaM6AvrBconsistently triggered a strong HR while other strains induced it at different intensities significantly depending on temperature. Both behaviors of low and warm temperature-dependency for T3SS efficiency were observed among thermosensitive strains, irrespective of theirin-vitrogrowth optimum. Surprisingly, differences were also observed among quasi-clonal strains. These results reveal a strongly strain-specific regulatory role of temperature in effector injection and reinforce the notion that the presence/absence of effectors is not sufficient to predict the outcome of plant-bacteria interactions. Moreover, this work highlights the necessity to study bacterial virulence in a broader set of strains insofar asPtoDC3000 is a reliable model strain but not representative of theP. syringaecomplex.Author summaryPseudomonas syringaeis a bacterium ubiquitous in the environment and responsible for important crop losses worldwide. Moreover,P. syringaeserves as a model organism for studying plant-pathogen interactions. Bacteria rely on various virulence mechanisms to successfully infect their host, one of the most important of which is the Type III Secretion System (T3SS). Although it is acknowledged that environmental conditions play a significant role in the plant-pathogen interactions, our understanding of their influence on both partners is still limited. Regarding temperature, contrasting findings have been reported about its influence on T3SS efficiency. While most efforts have focused on a few strains ofP. syringae, the phylogenetic diversity of this bacterium is enormous. Consequently, we decided to characterize the role of temperature on T3SS efficiency inP. syringaein a broader way. Our results showed that bacterial behavior in response to temperature is highly variable among strains, even among very closely related ones. Our study provides new insights into the role of temperature in regulating bacterial virulence and further evidence of the need to investigate the diversity of pathogenic organisms beyond model strains.