bluuebunny/crossref_metadata_2025 huggingface dataset:
Low Diversity in Nasal Microbiome Associated WithStaphylococcus aureusColonization and Bloodstream Infections in Hospitalized Neonates
Authors: Zhao Ni , Khamash Dina F , Koh Hyunwook , Voskertchian Annie , Egbert Emily , Mongodin Emmanuel F , White James R , Hittle Lauren , Colantuoni Elizabeth , Milstone Aaron M
Published: September 2021

Background

Staphylococcus aureus is a leading cause of infectious morbidity and mortality in neonates. Few data exist on the association of the nasal microbiome and susceptibility to neonatal S. aureus colonization and infection.

Methods

We performed 2 matched case–control studies (colonization cohort—neonates who did and did not acquire S. aureus colonization; bacteremia cohort—neonates who did [colonized neonates] and did not [controls] acquire S. aureus colonization and neonates with S. aureus bacteremia [bacteremic neonantes]). Neonates in 2 intensive care units were enrolled and matched on week of life at time of colonization or infection. Nasal samples were collected weekly until discharge and cultured for S. aureus, and the nasal microbiome was characterized using 16S rRNA gene sequencing.

Results

In the colonization cohort, 43 S. aureus–colonized neonates were matched to 82 controls. At 1 week of life, neonates who acquired S. aureus colonization had lower alpha diversity (Wilcoxon rank-sum test P < .05) and differed in beta diversity (omnibus MiRKAT P = .002) even after adjusting for birth weight (P = .01). The bacteremia cohort included 10 neonates, of whom 80% developed bacteremia within 4 weeks of birth and 70% had positive S. aureus cultures within a few days of bacteremia. Neonates with bacteremia had an increased relative abundance of S. aureus sequences and lower alpha diversity measures compared with colonized neonates and controls.

Conclusions

The association of increased S. aureus abundance and decrease of microbiome diversity suggest the need for interventions targeting the nasal microbiome to prevent S. aureus disease in vulnerable neonates.
Modeling phenological reaction norms over an elevational gradient reveals contrasting strategies of Dusky Flycatchers and Mountain Chickadees in response to early-season temperatures
Authors: Coe Sharon J , Purcell Kathryn L , Rotenberry John T
Published: September 2021

We developed an approach to distinguish among 3 alternative strategies that birds may employ relating the timing of egg laying across elevations to annual variation in spring temperature (phenological reaction norms), which we applied to analyze the breeding phenology of 2 species over an elevational gradient in the Sierra Nevada, California. In a “simple-offset” strategy, birds at different elevations initiate breeding relative to environmental temperature in a consistent manner, in that breeding onset is triggered by a critical temperature regardless of when it occurs in the spring. Elevation-specific reaction norms based on multiple years are offset (high-elevation birds start breeding later) but parallel. In a “delay” strategy, in cooler springs, populations at higher elevations that are sensitive to early-season weather-related risks delay laying onset relative to those at lower elevations, yielding a high-elevation reaction norm that diverges from a low-elevation one at cooler temperatures. Conversely, high-elevation populations in cooler springs that are sensitive to the risk of having insufficient time to complete a breeding cycle advance laying onset relative to lower populations (“advance” strategy), yielding a high-elevation reaction norm than converges with a low-elevation one. Both delay and advance strategies imply an elevation-dependent interaction between temperature and date (photoperiod) in influencing laying onset. Examined across 3 elevation groupings, phenological reaction norms of Mountain Chickadees (Poecile gambeli) were essentially parallel, consistent with simple offset, whereas Dusky Flycatchers (Empidonax oberholseri) relationships were more complex. In cooler springs, mid-elevation flycatchers bred comparatively late relative to lowest-elevation birds (delay), implying greater sensitivity to early-season risks, but still with sufficient time to complete a breeding cycle. However, high-elevation flycatchers bred comparatively early relative to mid-elevation populations (advance); delaying at these highest elevations may not be an option. Our approach revealed differences in risk sensitivity that were consistent with other ecological differences between the 2 species.
Electron microscopy for imaging organelles in plants and algae
Authors: Weiner Ethan , Pinskey Justine M , Nicastro Daniela , Otegui Marisa S
Published: September 2021

Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.
Exploring the relationship between political partisanship and COVID-19 vaccination rate
Authors: Ye Xinyuan
Published: September 2021

Background

Although increasing COVID-19 vaccination rates is critical to end the pandemic, vaccination goals are far from being achieved. Political partisanship may be a risk factor for getting the COVID-19 vaccine. This study examines the association between the political partisanship and vaccination rate at the county-level and quantifies the differences between the Democratic and Republican parties.

Methods

Data are from CDC, the NY Times, and the US Census and American Community Survey. Linear regressions are used to test the relationships between the political partisanship and COVID-19 vaccination rate at the county level. The dependent variable is the cumulative COVID-19 vaccination rate each month between January and August, 2021 and the explanatory variables are the county political partisanship and interaction terms between political partisanship and time dummies during the study period.

Results

Republican counties consistently had lower vaccination rates than Democratic counties, and the gap in vaccination rates between a typical Democratic and Republican county has steadily widened by month.

Conclusion

The COVID-19 vaccination rate is strongly associated with political partisanship. The political nature of this pandemic has created gaps in vaccination rates along party lines and will continue to be a barrier in mitigating this public health crisis.
Identification of ultrastructural signatures of sleep and wake in the fly brain
Authors: Flores Carlos C , Loschky Sophia S , Marshall William , Spano Giovanna Maria , Massaro Cenere Mariangela , Tononi Giulio , Cirelli Chiara
Published: September 2021

The cellular consequences of sleep loss are poorly characterized. In the pyramidal neurons of mouse frontal cortex, we found that mitochondria and secondary lysosomes occupy a larger proportion of the cytoplasm after chronic sleep restriction compared to sleep, consistent with increased cellular burden due to extended wake. For each morphological parameter, the within-animal variance was high, suggesting that the effects of sleep and sleep loss vary greatly among neurons. However, the analysis was based on 4–5 mice/group and a single section/cell. Here, we applied serial block-face scanning electron microscopy to identify signatures of sleep and sleep loss in the Drosophila brain. Stacks of images were acquired and used to obtain full 3D reconstructions of the cytoplasm and nucleus of 263 Kenyon cells from adult flies collected after a night of sleep (S) or after 11 h (SD11) or 35 h (SD35) of sleep deprivation (9 flies/group). Relative to S flies, SD35 flies showed increased density of dark clusters of chromatin and Golgi apparata and a trend increase in the percent of cell volume occupied by mitochondria, consistent with increased need for energy and protein supply during extended wake. Logistic regression models could assign each neuron to the correct experimental group with good accuracy, but in each cell, nuclear and cytoplasmic changes were poorly correlated, and within-fly variance was substantial in all experimental groups. Together, these results support the presence of ultrastructural signatures of sleep and sleep loss but underscore the complexity of their effects at the single-cell level.
Solving the Coral Species Delimitation Conundrum
Authors: Ramírez-Portilla Catalina , Baird Andrew H , Cowman Peter F , Quattrini Andrea M , Harii Saki , Sinniger Frederic , Flot Jean-François
Published: September 2021

Distinguishing coral species is not only crucial for physiological, ecological, and evolutionary studies but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that interspecific hybridization might be responsible for this apparent conundrum. Here, we used three lines of evidence—morphology, breeding trials, and molecular approaches—to identify species boundaries in a group of ecologically important tabular Acropora corals. In contrast to previous studies, our morphological analysis yielded groups that were congruent with experimental crosses as well as with coalescent-based and allele sharing-based multilocus approaches to species delimitation. Our results suggest that species of the genus Acropora are reproductively isolated and independently evolving units that can be distinguished morphologically. These findings not only pave the way for a taxonomic revision of coral species but also outline an approach that can provide a solid basis to address species delimitation and provide conservation support to a wide variety of keystone organisms. [Acropora; coral reefs; hybridization; reproductive isolation; taxonomy.]
Diagnostic Accuracy of Clinical Tests and Imaging Exams for Femoroacetabular Impingement: An Umbrella Review of Systematic Reviews
Authors: Fernandes Daniel A. , Melo Gilberto , Contreras Marcos E. K. , Locks Renato , Chahla Jorge , Neves Fabricio S.
Published: September 2021

Objective:

To synthesize available evidence about diagnostic accuracy of clinical tests and imaging examinations for femoroacetabular impingement (FAI) syndrome.

Design:

Umbrella review.

Setting:

N/A.

Participants:

N/A.

Interventions:

N/A.

Main Outcome Measures:

Systematic reviews (SR) indexed in Embase, LIVIVO, PubMed, SCOPUS, the Cochrane Library, and Web of Science were searched in a 2-phase process. SR assessing diagnostic accuracy were considered eligible.

Results:

From 1520 studies, 6 SR were included, which evaluated 24 primary studies related to FAI syndrome. Of these, 5 SR assessed clinical tests, and a substantial heterogeneity was found concerning reference standards adopted across primary studies, which included arthroscopy, clinical examination (associated or not with imaging exams), intra-articular injections, and open surgery. Most clinical tests presented higher values of sensitivity compared with specificity, although evidence was considered limited because the same primary studies were often included across SR. Nonetheless, evidence around the flexion adduction internal rotation (FADIR) test was considered stronger and its use as a screening tool was consistently supported. Only one SR assessed the accuracy of imaging examinations, which adopted open surgery as the sole reference standard. Most imaging exams presented considerably high values of sensitivity, although specificity values were notably lower.

Conclusions:

No robust recommendations can be provided for most clinical tests, although the FADIR test, in particular, was consistently supported as a screening tool. Moreover, although imaging examinations showed considerably high sensitivity values, evidence was considered sparse and further research is strongly recommended to validate its use as reference standards for diagnostic accuracy data.
Advanced cardiac life support: lessons from recent trials on how to move forward
Authors: Berg Katherine M. , Soar Jasmeet
Published: September 2021

Purpose of review

This review discusses potential reasons why many recent large trials in advanced cardiac life support have failed to demonstrate a difference in outcomes and suggests some points for consideration in planning future trials.

Recent findings

The ARREST trial, a small controlled trial studying the effect of intra-arrest extracorporeal membrane oxygenation (ECMO, or E-CPR) on survival and functional outcome in patients with refractory ventricular fibrillation cardiac arrest, was stopped after 30 patients for benefit. This stands in contrast to several recent trials enrolling up to several thousand patients and finding no difference. Three ways in which the ARREST trial approach differed from that of other recent trials, and how those differences may contribute to the possibility of detecting the benefit of an intervention, are discussed.

Refining our ability to select patients with potential to benefit from an intervention, providing those interventions earlier, and tailoring the specifics of an intervention to the individual patient all may be important in design of cardiac arrest trials, as illustrated by the large effect seen in the ARREST trial.
Perioperative renal protection
Authors: Saadat-Gilani Khaschayar , Zarbock Alexander
Published: September 2021

Purpose of review

Acute kidney injury (AKI) is a common but underestimated syndrome in the perioperative setting. AKI can be induced by different causes and is associated with increased morbidity and mortality. Unfortunately, no specific treatment options are available at the moment.

Recent findings

AKI is now understood as being a continuum ranging from normal kidney function over AKI and acute kidney disease to ultimately chronic kidney disease. The KDIGO organization recommend in 2012 implementation of preventive bundles in patients at high risk for AKI. In the perioperative setting, relevant measures include hemodynamic optimization, with careful consideration of blood pressure targets, adequate fluid therapy to maintain organ perfusion and avoidance of hyperglycaemia. These measures are most effective if patients at risk are identified as soon as possible and measures are implemented accordingly. Although current point of care functional biomarkers can detect patients at risk earlier than the established damage biomarkers, some components of the preventive bundle are still under investigation.

Good evidence exists for the use of biomarkers to identify individual patients at risk for AKI and for the implementation of haemodynamic optimization, abdication of nephrotoxins, adequate fluid administration using balanced crystalloid solutions and glycaemic control. The data for using colloids or the degree of nephrotoxicity of contrast media still remain inconclusive.
Definitions of acute renal dysfunction: an evolving clinical and biomarker paradigm
Authors: Ostermann Marlies , Wu VinCent , Sokolov Dmitry , Lumlertgul Nuttha
Published: September 2021

Purpose of review

The current definition and classification of acute kidney injury (AKI) has limitations and shortcomings, which impact clinical management. The aim of this review is to highlight recent advances in our understanding of the pathophysiology and epidemiology of AKI, which impacts management and offers opportunities.

Recent findings

Kidney damage varies according to the type of primary insult, secondary effects and mitigating responses and leads to distinct molecular, cellular and functional changes. Different sub-types of AKI with varying clinical phenotypes, recovery patterns and responses to therapeutic interventions have been identified. New tools to identify and characterize these AKI sub-types are available with the potential opportunity for individualized timely aetiology-based management of AKI.

The identification of different sub-phenotypes of AKI based on genetic, molecular, cellular and functional pathophysiological changes following potential nephrotoxic exposures is possible with new technologies. This offers opportunities for personalized management of AKI and supports the call for a refinement of the existing AKI criteria.
Increased Use of Anti‐Tumor Necrosis Factor Following the Implementation of the ECCO–ESPGHAN Guidelines and its Impact on the Outcome of Pediatric Crohn's Disease
Authors: D'Arcangelo Giulia , Abi Nader Elie , Charbit‐Henrion Fabienne , Talbotec Cécile , Goulet Olivier , Ruemmele Frank M. , Pigneur Bénédicte
Published: September 2021

Objectives:

The first ECCO‐ESPGHAN guidelines for the medical management of pediatric Crohn disease (CD) were published in 2014. Whether their implementation, and the consequent increased use of an upfront anti‐tumor necrosis factor therapy, have changed the course of the disease has not been investigated yet. We aimed at comparing the evolution of pediatric CD patients diagnosed and treated before and after 2014.

Methods:

Single‐center retrospective study including all children diagnosed with CD from January 2010 to December 2018. Patients diagnosed between 2010 and 2014 (group 1) were compared to those diagnosed after 2014 (group 2). For each patient, at baseline and every 6‐month, number of relapses, the occurrence of complication, therapy received and biological parameters were noted, as well as any endoscopic or radiologic evaluation.

Results:

One hundred and fifty‐four patients were included in the analysis, 78 (51%) diagnosed after 2014. The cumulative probability of a relapse‐free and surgery‐free course was significantly higher for patients treated according to the guidelines (log rank hazard ratio [HR] = 1,818, P = 0.003 and HR = 3,15, 95% confidence interval, P = 0.04, respectively). Mucosal healing rate was significantly higher among patients of group 2 at 1 and 2 years (P = 0.04 and P = 0.05, respectively), while no significant difference was observed for transmural healing rates, as well as for the risk of complications.

Conclusions:

The implementation of the 2014 CD guidelines appears to have a significant impact on disease outcomes, with a significantly lower risk for relapse and surgery, while no effect could be observed on the risk of developing complications.
Pulmonary Open, Robotic, and Thoracoscopic Lobectomy (PORTaL) Study
Authors: Kent Michael S. , Hartwig Matthew G. , Vallières Eric , Abbas Abbas E. , Cerfolio Robert J. , Dylewski Mark R. , Fabian Thomas , Herrera Luis J. , Jett Kimble G. , Lazzaro Richard S. , Meyers Bryan , Mitzman Brian A. , Reddy Rishindra M. , Reed Michael F. , Rice David C. , Ross Patrick , Sarkaria Inderpal S. , Schumacher Lana Y. , Tisol William B. , Wigle Dennis A. , Zervos Michael
Published: September 2021

Objective:

The aim of this study was to analyze outcomes of open lobectomy (OL), VATS, and robotic-assisted lobectomy (RL).

Summary Background Data:

Robotic-assisted lobectomy has seen increasing adoption for treatment of early-stage lung cancer. Comparative data regarding these approaches is largely from single-institution case series or administrative datasets.

Methods:

Retrospective data was collected from 21 institutions from 2013 to 2019. All consecutive cases performed for clinical stage IA-IIIA lung cancer were included. Neoadjuvant cases were excluded. Propensity-score matching (1:1) was based on age, sex, race, smoking-status, FEV1%, Zubrod score, American Society of Anesthesiologists score, tumor size, and clinical T and N stage.

Results:

A total of 2391 RL, 2174 VATS, and 1156 OL cases were included. After propensity-score matching there were 885 pairs of RL vs OL, 1,711 pairs of RL vs VATS, and 952 pairs of VATS vs OL. Operative time for RL was shorter than VATS (P < 0.0001) and OL (P = 0.0004). Compared to OL, RL and VATS had less overall postoperative complications, shorter hospital stay (LOS), and lower transfusion rates (all P<0.02). Compared to VATS, RL had lower conversion rate (P<0.0001), shorter hospital stay (P<0.0001) and a lower postoperative transfusion rate (P =0.01). RL and VATS cohorts had comparable postoperative complication rates. In-hospital mortality was comparable between all groups.

Conclusions:

RL and VATS approaches were associated with favorable perioperative outcomes compared to OL. Robotic-assisted lobectomy was also associated with a reduced length of stay and decreased conversion rate when compared to VATS.
Moderate to Severe Soft Tissue Diabetic Foot Infections
Authors: Pham Truong-Thanh , Gariani Karim , Richard Jean-Christophe , Kressmann Benjamin , Jornayvaz François R. , Philippe Jacques , Lipsky Benjamin A. , Uçkay Ilker
Published: September 2021

Background:

The optimal duration of antibiotic therapy for soft-tissue infections of the diabetic foot remains unknown.

Objective:

We determine if antibiotic therapy after debridement for a short (10 days), compared with a long (20 days), duration for soft-tissue infections of the diabetic foot results in similar rates of clinical remission and adverse events (AE).

Summary of Background Data:

The optimal duration of systemic antibiotic therapy, after successful debridement, for soft tissue infections of diabetic patients is unknown. Because of the high recurrence risk, overuse is commonplace.

Methods:

This was a randomized, controlled, non-inferiority pilot trial of cases of diabetic foot infection (excluding osteomyelitis) with the primary outcome of “clinical remission at 2-months follow-up”.

Results:

Among 66 enrolled episodes (17% females; median age 71 years), we randomized 35 to the 10-day arm and 31 to the 20-day arm. The median duration of the parenteral antibiotic therapy was 1 day, with the remainder given orally. In the intention-to-treat population, we achieved clinical remission in 27 (77%) patients in the 10-day arm compared to 22 (71%) in the 20-days arm (P = 0.57). There were a similar proportion in each arm of AE (14/35 versus 11/31; P = 0.71), and remission in the per-protocol population (25/32 vs 18/27; P = 0.32). Overall, 8 soft tissue DFIs in the 10-day arm and 5 cases in the 20-day arm recurred as a new osteomyelitis [8/35 (23%) versus 5/31 (16%); P = 0.53]. Overall, the number of recurrences limited to the soft tissues was 4 (6%). By multivariate analysis, rates of remission (intention-to-treat population, hazard ratio 0.6, 95%CI 0.3-1.1; per-protocol population 0.8, 95%CI 0.4-1.5) and AE were not significantly different with a 10-day compared to 20-day course.

Conclusions:

In this randomized, controlled pilot trial, post-debridement antibiotic therapy for soft tissue DFI for 10 days gave similar (and non-inferior) rates of remission and AEs to 20 days. A larger confirmatory trial is under way.

Trial registration:

ClinicalTrials NCT03615807.
“The Story I Will Never Forget”
Authors: Sandhu Harminder , Foote Darci C. , Evans Julie , Santosa Katherine B. , Kemp Michael T. , Donkersloot John N. , White Erin M. , Mazer Laura M. , Sandhu Gurjit
Published: September 2021

Objective:

We sought to better understand what defines a critical incident experience for the surgical trainee.

Summary Background Data:

Critical incidents are formative moments stamped indelibly on one's memory that shape professional identity. The critical incident technique—using participants’ narratives to identify patterns and learn from their perceptions—has been explored in some healthcare settings, but there has been no inquiry within surgery.

Methods:

Surgical residents at 5 residency programs (1 community, 1 university-affiliated, 3 university) were surveyed using an online questionnaire from November to December 2020. Convenience sampling was used to identify the study population. Participants were invited to write about formative, impactful experiences in training. Interpretive description was the qualitative methodology used to locate information, analyze, and record patterns in the data. Individual responses were categorized and assessed for overlying themes.

Results:

Overall, 28 narratives were collected from surgery residents in 3 specialties (general surgery, plastic surgery, and urology), with postgraduate year representation of post-graduate years 1 to 6. Respondents were 40% female. Nineteen of the narratives reported a negative experience. Four themes were identified from responses: 1) growth through personal self-reflection, 2) difficult interpersonal interactions, 3) positive team dynamics as a psychological safety net, and 4) supportive program cultures that promote learning.

Conclusions:

Critical incident narratives among surgical residents indicate that unforgettable and formative experiences—both positive and negative— occur in 4 domains: within the individual, within a relationship, among a team, and within a program. Further exploring these domains in surgical training will inform optimal educational programming to support trainee development and wellbeing.
Local Exhaust Ventilation to Control Dental Aerosols and Droplets
Authors: Allison James R , Dowson Christopher , Pickering Kimberley , Červinskytė Greta , Durham Justin , Jakubovics Nicholas S , Holliday Richard
Published: September 2021

Dental procedures produce aerosols which may remain suspended and travel significant distances from the source. Dental aerosols and droplets contain oral microbes and there is potential for infectious disease transmission and major disruption to dental services during infectious disease outbreaks. One method to control hazardous aerosols often used in industry is Local Exhaust Ventilation (LEV). The aim of this study was to investigate the effect of LEV on aerosols and droplets produced during dental procedures. Experiments were conducted on dental mannequins in an 825.4 m3 open plan clinic, and a 49.3 m3 single surgery. 10-minute crown preparations were performed with an air-turbine handpiece in the open plan clinic, and 10-minute full mouth ultrasonic scaling in the single surgery. Fluorescein was added to instrument irrigation reservoirs as a tracer. In both settings, Optical Particle Counters (OPCs) were used to measure aerosol particles between 0.3 – 10.0 μm and liquid cyclone air samplers were used to capture aerosolised fluorescein tracer. Additionally, in the open plan setting fluorescein tracer was captured by passive settling onto filter papers in the environment. Tracer was quantified fluorometrically. An LEV device with High Efficiency Particulate Air (HEPA) filtration and a flow rate of 5,000 L/min was used. LEV reduced aerosol production from the air-turbine handpiece by 90% within 0.5 m, and this was 99% for the ultrasonic scaler. OPC particle counts were substantially reduced for both procedures, and air-turbine settled droplet detection reduced by 95% within 0.5 m. The effect of LEV was substantially greater than suction alone for the air-turbine and was similar to the effect of suction for the ultrasonic scaler. LEV reduces aerosol and droplet contamination from dental procedures by at least 90% in the breathing zone of the operator and it is therefore a valuable tool to reduce the dispersion of dental aerosols.
Antelope space-use and behavioural responses to varying anthropogenic influences may permit long-term persistence in a highly human-dominated landscape
Authors: Jha Rohit Raj , Isvaran Kavita
Published: September 2021

The only means of conserving a species or a habitat in a human-dominated landscape is through promoting coexistence while minimizing conflict. To achieve this, it is vital to understand how wildlife are impacted by direct and indirect human activities. Such information is relatively rare from areas with high human densities. To investigate how animals respond to altered ecological conditions in human-dominated landscapes, we focussed on a wild herbivore of conservation concern in Krishnasaar Conservation Area (KrCA) in Nepal. Here, blackbuck Anticope cervicapra, a generalist grazer, lives in refugia located in a growing human population. We studied the impacts of humans on habitat-use and behaviour of blackbuck. We laid 250 × 250 m grid cells in the entire KrCA and carried out indirect sign surveys with three replications for habitat-use assessment. We observed herds of blackbuck for 89 hours in different possible habitat types, location and time of the day using scan sampling methods. Our habitat-use survey showed that habitats under intensive human use were hardly used by blackbuck, even when high-quality forage was available. In areas with low levels of human activity, natural risk factors, primarily habitat openness, was the major predictor of habitat-use. Interestingly, livestock presence positively influenced habitat-use by blackbuck. Blackbuck were substantially more vigilant when they were in forest than in grassland, again indicating an influence of risk. Overall, blackbuck appear to be sensitive to risk associated with both natural and anthropogenic factors. Our findings have direct implications for managing human-wildlife interactions in this landscape, specifically regarding strategies for livestock grazing in habitats highly used by blackbuck and concerning predictions of how changing land-use will impact long-term persistence of blackbuck. Our work suggests that wild herbivores may be able to persist in landscapes with high human densities so long as there are refuges where levels of human activity are relatively low.
Evaluating an internet-delivered fear conditioning and extinction protocol using response times and affective ratings
Authors: Björkstrand Johannes , Pine Daniel S. , Frick Andreas
Published: September 2021

Pavlovian fear conditioning is widely used to study mechanisms of fear learning, but high-throughput studies are hampered by the labor-intensive nature of examining participants in the lab. To circumvent this bottle-neck, fear conditioning tasks have been developed for remote delivery. Previous studies have examined remotely delivered fear conditioning protocols using expectancy and affective ratings. Here we replicate and extend these findings using an internet-delivered version of the Screaming Lady paradigm, evaluating the effects on negative affective ratings and response time to an auditory probe during stimulus presentations. In a sample of 80 adults, we observed clear evidence of both fear acquisition and extinction using affective ratings. Response times were faster when probed early, but not later, during presentation of stimuli paired with an aversive scream. The response time findings are at odds with previous lab-based studies showing slower responses to threat-predicting cues. The findings underscore the feasibility of employing remotely delivered fear conditioning paradigms with affective ratings as outcome, and highlight the need for further research examining optimal parameters for concurrent response time measures or alternate modes of non-verbal estimation of conditioned responses in Pavlovian conditioning protocols.
Diversity and Metabolic Potential of Microbial Communities in a Serpentinite-Hosted Spring at the Tablelands
Authors: Dart Emily , Brazelton William J.
Published: September 2021

The geochemical process of serpentinization releases energy and organic carbon: two of the basic requirements needed to support life. Sites of active serpentinization in the deep subsurface provide the intriguing possibility of a non-photosynthetically-supported biosphere. However, serpentinization also creates conditions, such as high pH and limited electron acceptors, which may limit microbial growth and diversity. Gaining an understanding of the identity and metabolic potential of microbes that thrive in these environments may provide insight as to whether serpentinization is sufficient to independently support life. Tablelands Ophiolite in Gros Morne National Park, Newfoundland, Canada is a continental site of serpentinization where serpentinite springs form surface pools. These pools provide easy sampling access to subsurface fluids and may allow for sampling of the subsurface microbial community. However, identification of members of the subsurface community in these pools is complicated by both surface contamination and contamination by organisms that inhabit the transition zone where hydrogen-rich subsurface fluids meet oxygen-rich surface fluids. This study was designed to distinguish among these potential sources of microorganisms by using a sampling technique that more effectively samples subsurface fluids. Community dissimilarity comparisons using environmental 16S rRNA gene sequencing indicate that the sampling design led to more direct access to subsurface fluids. These results are supported by metagenomic analyses that show metabolic pathways consistent with non-photosynthetic carbon fixation in the samples expected to represent subsurface fluids and that show hydrogen oxidation pathways in samples associated with the surface sources. These results provide a clearer picture of the diversity and metabolic potential of microbial communities potentially inhabiting subsurface, serpentinite-hosted habitats.
Variation in colour signals amongSarraceniapitcher plants and the potential role of areoles in the attraction of flying Hymenoptera
Authors: Dupont Corentin , Villemant Claire , Hatterman Tom , Pratviel Jeremie , Gaume Laurence , Gomez Doris
Published: September 2021

Sarraceniainsectivorous plants show a diversity of visual features in their pitchers but their perception by insects and their role in attraction, have received little attention. They also vary in prey composition, with some species trapping more flying Hymenoptera, such as bees. To test the hypothesis of a link between visual signal variability and prey segregation ability, and to identify which signal could attract flying Hymenoptera, we characterised, the colour patterns of 32 pitchers belonging to four taxa, modelled their perception by flying Hymenoptera, and examined the prey they trapped. The pitchers of the four taxa differed in colour patterns, with notably two long-leaved taxa displaying clear areoles, which contrasted strongly in colour and brightness with the vegetative background and with other pitcher areas in the eyes of flying Hymenoptera. These taxa trapped high proportion of flying hymenoptera. This suggests that contrasting areoles may act as a visual lure for flying Hymenoptera, making plants particularly visible to these insects. Prey capture also differed according to pitcher stage, morphology, season and visual characteristics. Further studies on prey visitation are needed to better understand the link between prey capture and attraction feature.
Principles governing the topological organization of object selectivities in ventral temporal cortex
Authors: Zhang Yiyuan , Zhou Ke , Bao Pinglei , Liu Jia
Published: September 2021

To achieve the computational goal of rapidly recognizing miscellaneous objects in the environment despite large variations in their appearance, our mind represents objects in a high-dimensional object space to provide separable category information and enable the extraction of different kinds of information necessary for various levels of the visual processing. To implement this abstract and complex object space, the ventral temporal cortex (VTC) develops different object-selective regions with certain topological organization as the physical substrate. However, the principle that governs the topological organization of object selectivities in the VTC remains unclear. Here, equipped with the wiring cost minimization principle constrained by the wiring length of neurons in human temporal lobe, we constructed a hybrid self-organizing map (SOM) model as an artificial VTC (VTC-SOM) to explain how the abstract and complex object space is faithfully implemented in the brain. In two in silico experiments with the empirical brain imaging and single-unit data, our VTC-SOM predicted the topological structure of fine-scale functional regions (face-, object-, body-, and place-selective regions) and the boundary (i.e., middle Fusiform Sulcus) in large-scale abstract functional maps (animate vs. inanimate, real-word large-size vs. small-size, central vs. peripheral), with no significant loss in functionality (e.g., categorical selectivity, a hierarchy of view-invariant representations). These findings illustrated that the simple principle utilized in our model, rather than multiple hypotheses such as temporal associations, conceptual knowledge, and computational demands together, was apparently sufficient to determine the topological organization of object-selectivities in the VTC. In this way, the high-dimensional object space is implemented in a two-dimensional cortical surface of the brain faithfully.
A novel, computationally tractable algorithm flags in big matrices every column associated in any way with others or a dependent variable, with much higher power when columns are linked like mutations in chromosomes
Authors: Antezana Marcos A.
Published: September 2021

When a data matrix DM has many independent variables IVs, it is not computationally tractable to assess the association of every distinct IV subset with the dependent variable DV of the DM, because the number of subsets explodes combinatorially as IVs increase. But model selection and correcting for multiple tests is complex even with few IVs.

DMs in genomics will soon summarize millions of mutation markers and genomes. Searching exhaustively in such DMs for markers that alone or synergistically with others are associated with a trait is therefore computationally tractable only for 1- and 2-marker effects. Also population geneticists study mainly 2-marker combinations.

I present a computationally tractable, fully parallelizable Participation in Association Score (PAS) that in a DM with markers detects one by one every column that is strongly associated in any way with others. PAS does not examine column subsets and its computational cost grows linearly with the number of columns, remaining reasonable even when DMs have millions of columns.

PAS exploits how associations of markers in the rows of a DM cause associations of matches in the rows’ pairwise comparisons. For every such comparison with a match at a tested column, PAS computes the matches at other columns by modifying the comparison’s total matches (scored once per DM), yielding a distribution of conditional matches that reacts diagnostically to the associations of the tested column. Equally computationally tractable is dvPAS that flags DV-associated IVs by also probing the matches at the DV.

P values for the scores are readily obtained by permutation and accurately Sidak-corrected for multiple tests, bypassing model selection. The P values of a column’s PASs for different orders of association are i.i.d. and readily turned into a single P value.

Simulations show that i) PAS and dvPAS generate uniform-(0,1)-distributed type I error in null DMs and ii) detect randomly encountered binary and trinary models of significant n-column association and n-IV association with a binary DV, respectively, with power in the order of magnitude of exhaustive evaluation’s and false positives that are uniform-(0,1)-distributed or straightforwardly tuned to be so. Power to detect 2-way associations that extend over 100+ columns is non-parametrically ultimate but that to detect pure n-column associations and pure n-IV DV associations sinks exponentially as n increases.

Important for geneticists, dvPAS power increases about twofold in trinary vs. binary DMs and by orders of magnitude with markers linked like mutations in chromosomes, specially in trinary DMs where furthermore dvPAS fine-maps with highest resolution.
abmR: an R package for agent-based model analysis of large-scale movements across taxa
Authors: Gochanour Benjamin , Fernández-López Javier , Contina Andrea
Published: September 2021

Agent-based modeling (ABM) shows promise for animal movement studies. However, a robust, open-source, and spatially explicit ABM coding platform is currently lacking.

We present abmR, an R package for conducting continental-scale ABM simulations across animal taxa. The package features two movement functions, each of which relies on the Ornstein-Uhlenbeck (OU) process.

The theoretical background for abmR is discussed and the main functionalities are illustrated using example populations.

Potential future additions to this open-source package may include the ability to specify multiple environmental variables or to model interactions between agents. Additionally, updates may offer opportunities for disease ecology and integration with other R movement modeling packages.
Intestinal epithelial IPMK protects mice from experimental colitis via governing colonic tuft cell development
Authors: Park Seung Eun , Jeong Jae Woong , Lee Su-Hyung , Park Seung Ju , Ryu Jaeseung , Oh Se Kyu , Fang Sungsoon , Kim Seyun
Published: September 2021

As a pleiotropic signaling factor, inositol polyphosphate multikinase (IPMK) is involved in key biological events such as growth and innate immunity, acting either enzymatically to mediate the biosynthesis of inositol polyphosphates and phosphatidylinositol 3,4,5-trisphosphates, or noncatalytically to control key signaling target molecules. However, the functional significance of IPMK in regulating gut epithelial homeostasis remains largely unknown. Here we show that intestinal epithelial-specific deletion of IPMK aggravates dextran sulfate sodium (DSS)-induced colitis with higher clinical colitis scores and elevated epithelial barrier permeability. No apparent defects in PI3K-AKT signaling pathway and pro-inflammatory cytokine production were found in IPMK-deficient colons challenged by DSS treatment. RNA-sequencing and FACS analyses further revealed significantly decreased tuft cells in IPMK-deficient colons. Importantly, IPMK deletion in the gut epithelium was found to decrease choline acetyltransferase (ChAT) but not IL-25, suggesting selective loss of cholinergic signaling. Thus, these findings identify IPMK as a physiological determinant of tuft cell differentiation and highlight the critical function of IPMK in the control of gut homeostasis.
β-Catenin-NFκB-CFTR interactions in cholangiocytes regulate inflammation and fibrosis during ductular reaction
Authors: Hu Shikai , Russell Jacquelyn O. , Liu Silvia , Rai Ravi , Kosar Karis , Tao Junyan , Hurley Edward , Poddar Minakshi , Singh Sucha , Bell Aaron , Shin Donghun , Raeman Reben , Singhi Aatur D. , Nejak-Bowen Kari , Ko Sungjin , Monga Satdarshan P.
Published: September 2021

Expansion of biliary epithelial cells (BECs) during ductular reaction (DR) is observed in liver diseases including cystic fibrosis (CF), and associated with inflammation and fibrosis, albeit without complete understanding of underlying mechanism. Using two different genetic knockouts of β-catenin, one with β-catenin loss is hepatocytes and BECs (KO1), and another with loss in only hepatocytes (KO2), we demonstrate disparate long-term repair after an initial injury by 2-week choline-deficient ethionine- supplemented diet. KO2 show gradual liver repopulation with BEC-derived β-catenin- positive hepatocytes, and resolution of injury. KO1 showed persistent loss of β-catenin, NF-κB activation in BECs, progressive DR and fibrosis, reminiscent of CF histology. We identify interactions of β-catenin, NFκB and CF transmembranous conductance regulator (CFTR) in BECs. Loss of CFTR or β-catenin led to NF-κB activation, DR and inflammation. Thus, we report a novel β-catenin-NFκB-CFTR interactome in BECs, and its disruption may contribute to hepatic pathology of CF.
MPTHub: an open-source software for characterizing the transport of particles in biorelevant media
Authors: Gabriel Leandro , Almeida Helena , Avelar Marta , Sarmento Bruno , das Neves José
Published: September 2021

The study of the transport of particles in different environments plays an essential role in understanding interactions with humans and other living organisms. Importantly, obtained data can be directly used for multiple applications in fields such as fundamental biology, toxicology or medicine. Particle movement in biorelevant media can be readily monitored using microscopy and converted into time-resolved trajectories using freely available tracking software. However, translation into tangible and meaningful parameters is time-consuming and not always intuitive. Thus, we developed a new software – MPTHub – as an open-access, stand-alone, user-friendly tool for the rapid and reliable analysis of particle trajectories extracted from video microscopy. The software was programmed using Python and allowed to import and analyze trajectory data, and export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. Data processing was reliable, fast (total processing time of less than 10 sec) and required minimal memory resources (up to a maximum of around 150 MB in RAM). Demonstration of software applicability was conducted by studying the transport of different polystyrene nanoparticles (100-200 nm) in mucus surrogates. Overall, MPTHub represents a freely available software tool that can be used even by unexperienced users for studying the transport of particles in biorelevant media.
Delayed implantation induced by letrozole in mice
Authors: Wang Fang , Li Shijie , Meng Lingshuai , Kuang Ye , Liu Zhonghua , Ma Xinghong
Published: September 2021

Implantation timing is key for a successful pregnancy. Short delay in embryo implantation caused by targeted gene ablation produced a cascading problem in the later stages of the pregnancy. Although several delayed implantation models have been established in wild mice, almost none of them is suitable for investigating the delay on the late events of pregnancy. Here, we report a new delayed implantation model established by the intraperitoneally administration of letrozole at 5 mg/kg body weight on the day 3 of pregnancy. In these mice, initiation of implantation was induced at will by the injection of estradiol (E2). When the estradiol (3 ng) was injected on day 4 of pregnancy (i.e., without delay), the embryo implantation restarted, and the pregnancy continued normally. However, high dose of estrogen (25 ng) caused compromised implantation. We also found that only 67% of the female mice could be pregnant normally and finally gave birth when the injection of estradiol (3 ng) was on day 5 of pregnancy (i.e., one day delay). Most of the failed pregnancies had impaired decidualization, decreased plasma progesterone levels and compromised angiogenesis. Progesterone supplementation could rescue decidualization failure in the mice. Collectively, we established a new model of delayed implantation by letrozole, which can be easily used to study the effect and mechanisms of delay of embryo implantation on the progression of late pregnancy events.