bluuebunny/crossref_metadata_2025 huggingface dataset:
Mild Thrombocytopenia, a Predictor of Outcomes After Laparoscopic Cholecystectomy
Authors: Reiche William S. , Walters Ryan W. , Schutte Bryce F. , Mukherjee Sandeep , Buaisha Haitam M.
Published: September 2023

Background:

A common cause of mild thrombocytopenia is chronic liver disease, the most common etiology being metabolic dysfunction–associated steatotic liver disease (MASLD). Mild thrombocytopenia is a well-defined, independent marker of hepatic fibrosis in patients with chronic liver disease. Currently, there is a paucity of information available to characterize perioperative risk in patients with MASLD; therefore, the characterization of perioperative morbidity is paramount. We used a platelet threshold of 150×109 as a surrogate for fibrosis in patients undergoing laparoscopic cholecystectomy to study its effect on perioperative complications and mortality.

Patients and Methods:

We queried the American College of Surgeons National Surgical Quality Improvement Program database for laparoscopic cholecystectomies occurring from 2005 through 2018. Demographic differences between patients with and without thrombocytopenia were evaluated using the t test or the χ2 test, whereas adjusted and unadjusted differences in outcome risk were evaluated using log-binomial regression models.

Results:

We identified 437,630 laparoscopic cholecystectomies of which 6.9% included patients with thrombocytopenia. Patients with thrombocytopenia were more often males, older, and with chronic disease. Patients with thrombocytopenia and higher Aspartate Aminotransferase to Platelet Ratio Index scores had 30-day mortality rates risk ratio of 5.3 (95% CI: 4.8-5.9), with higher complication rates risk ratio of 2.4 (95% CI: 2.3-2.5). The most frequent complications included the need for transfusion, renal, respiratory, and cardiac.

Conclusions:

Perioperatively, patients with mild thrombocytopenia undergoing laparoscopic cholecystectomy had higher mortality rates and complications compared with patients with normal platelet counts. Thrombocytopenia may be a promising, cost-effective tool to identify patients with MASLD and estimate perioperative risk, especially if used in high-risk populations.
Unique clinical challenges for the teenager with congenital heart disease
Authors: Pastor Tony , Elder Robert W.
Published: September 2023

Purpose of review

On top of existing rites of passage, adolescents with congenital heart disease (CHD) face additional challenges as related to their underlying medical condition. These include compliance with medications and appointments, establishing heart-healthy behaviors, navigating potential at-risk situations, and transition to adult-oriented care.

Recent findings

Teenagers with CHD should focus on the importance of exercise as this seems to have important long-term benefits and may help improve weight management. Mental health concerns are a major issue for teens with CHD and awareness and appropriate screening are critical. Discussion regarding sexual health, contraception, pregnancy, and CHD risk in offspring occur rarely in clinical practice, and their absence sets up the CHD adolescent for potential complications. Establishing patterns of trust and communication between physicians and teenage CHD patients are critical to enable the appropriate transition of care to adult congenital care, yet gaps in transition remain common.

The outpatient cardiologist has a critical role to help the teenager with CHD navigate difficult terrain. Returning to the roots of careful history taking, motivational interviewing, and open-ended questions may be of great benefit in warding off complications and helping steer the adolescent with CHD towards a life as a successful adult living with CHD.
A Rare Case of BRAF-mutated Metastatic Pleomorphic Xanthoastrocytoma Patient who Developed Radiodermatitis After Receiving Anti-BRAF Treatment
Authors: Atahan Ceren , Arslantas Esra , Ersen Danyeli Ayca , Celik Levent , Bozkurt Gokhan , Ugurluer Gamze , Corapcioglu Funda Vesile , Ozyar Enis
Published: September 2023

Pleomorphic xanthoastrocytoma (PXA) is a rare type of grade 2 or 3 brain tumor that usually occurs in children and young adults. The standard treatment for PXA is maximally safe resection, usually with adjuvant radiation therapy, for high-grade tumors. BRAF V600E mutation is one of the most common molecular alterations in these tumors, with nearly 70% of cases carrying this mutation. Although BRAF inhibitors have shown promise in treating progressive or refractory disease, their use has been associated with various adverse effects, including radiodermatitis, which is a relatively common complication. This paper presents a case of a 16-year-old male patient with BRAF-mutated metastatic PXA, who developed mild radiodermatitis after receiving BRAF inhibitors with concurrent radiation therapy.
Severe Acute Kidney Injury in Children as a Rare Complication of Paroxysmal Cold Hemoglobinuria
Authors: Zieg Jakub , Flachsová Eva , Linhartová Eva , Konopásek Patrik , Štolbová Šárka , Šimánková Naděžda , Fencl Filip , Pavlíček Petr , Suková Martina
Published: September 2023

Paroxysmal cold hemoglobinuria (PCH) is a rare condition in childhood characterized by complement-mediated premature destruction of red blood cells. PCH is associated with intravascular hemolysis causing hemoglobinuria, which may result in acute kidney injury of various severity. We aimed to retrospectively analyze clinical and laboratory features of children with PCH-associated acute kidney injury received at tertiary Pediatric Hematology and Nephrology Center, University Motol Hospital, Prague, Czech Republic during the period 2016 to 2022. We present here 3 children with PCH-associated acute kidney failure requiring renal replacement therapy. We highlight the association of PCH with kidney disease. Renal parameters and urine examination should be regularly tested in all children with PCH.
Incidence and Clinicopathologic Characteristics of Human Papillomavirus–independent Invasive Squamous Cell Carcinomas of the Cervix
Authors: Stolnicu Simona , Allison Douglas , Praiss Aaron M. , Tessier-Cloutier Basile , Momeni Boroujeni Amir , Flynn Jessica , Iasonos Alexia , Serrette Rene , Hoang Lien , Patrichi Andrei , Terinte Cristina , Pesci Anna , Mateoiu Claudia , Lastra Ricardo R. , Kiyokawa Takako , Ali-Fehmi Rouba , Kheil Mira , Oliva Esther , Devins Kyle M. , Abu-Rustum Nadeem R. , Soslow Robert A.
Published: September 2023

We aimed to determine the frequency of human papillomavirus–independent (HPVI) cervical squamous cell carcinoma (SCC) and to describe clinicopathologic characteristics. Among 670 patients with surgically treated SCCs in an established multi-institutional cohort, 447 had available tissue. Tissue microarrays were constructed and studied by in situ hybridization (ISH) for high-risk and low-risk human papillomavirus (HPV) mRNA and immunohistochemistry for p16 and p53. Tumors were HPVI if negative by HPV ISH and they failed to show diffuse p16 positivity by immunohistochemistry, and human papillomavirus–associated (HPVA) if positive by HPV ISH. Ten HPVI SCCs and 435 HPVA SCCs were identified; 2 cases were equivocal and excluded from analysis. The overall rate of HPVI SCC was low (2%) but was higher among older patients (7% in patients above 60 y of age and 17% in patients above 70 y of age). Compared with HPVA, patients with HPVI SCC were significantly older (median age, 72 vs. 49, P<0.001) and diagnosed at a higher stage (40% vs. 18% with stage III/IV disease, P=0.055). p53 expression was varied; 2 cases (20%) had null expression and 8 (80%) had wild-type expression. HPVI SCCs were heterogenous, with keratinizing, nonkeratinizing, and warty morphologies observed. Several cases had a precursor lesion reminiscent of differentiated vulvar intraepithelial neoplasia, with prominent basal atypia and hypereosinophilia or a basaloid-like morphology. Two patients (20%) had distant recurrences within 12 months, and 3 (30%) died of disease during follow-up. HPVI SCCs are rare tumors that are more common among older patients with higher stage disease and have important clinical and histologic differences from HPVA SCCs.
Neurologic infections in people with HIV: shifting epidemiological and clinical patterns
Authors: Wan Miranda Mengyuan , Gill M. John , Fonseca Kevin , Krentz Hartmut , Power Christopher , Lang Raynell
Published: September 2023

Objectives:

The aim of this study was to define the frequency, risk factors, and clinical outcomes of both AIDS-defining and non-AIDS-defining neurologic infections among people with HIV (PWH).

Design:

We conducted a retrospective observational cohort study by linking the clinical database at the Southern Alberta HIV Clinic (SAC) with the regional hospital and microbiology databases to identify cases and the associated morbidity and mortality for these neurologic infections from 1995 to 2018.

Methods:

Neurologic infections were categorized into AIDS-defining and non-AIDS defining. Annual incidence rates per 1000 person-years were calculated. Cox proportional hazards models estimated adjusted hazard ratios (aHR) and 95% confidence intervals of risk factors for neurologic infections in PWH and mortality outcomes.

Results:

Among 2910 PWH contributing 24 237 years of follow-up, 133 (4.6%) neurologic infections were identified; 107 (80%) were AIDS-defining and 26 (20%) non-AIDS defining. While the incidence of AIDS-defining neurologic infections declined over time, no change was seen in incidence of non-AIDS defining infections. The risk of having any neurologic infection was greater among black PWH (aHR = 2.5 [1.6–4.0]) (vs. white PWH) and those with a CD4+ T-cell nadir of less than 200 cells/μl (aHR = 6.6 [4.0–11.1]) (vs. ≥200 cells/μl). More AIDS-defining neurologic infections occurred in PWH with lower CD4+ T-cell counts and higher HIV viral loads. PWH with any neurologic infections experienced more seizures, strokes, all-cause mortality (aHR = 2.2 [1.5–3.2] and HIV-related mortality (aHR = 6.4 [3.9–10.7] (vs. no neurologic infection).

Conclusion:

Both AIDS and non-AIDS defining neurologic infections continue to occur in PWH resulting in significant morbidity and mortality. Early diagnosis and initiation of ART remain crucial in preventing neurological infections in PWH.
Using serial cross-sectional surveys to create a retrospective nested cohort to determine HIV incidence from 20 US cities
Authors: Burnett Janet C. , Broz Dita , Berg Julie , Callens Steven , Wejnert Cyprian
Published: September 2023

Objective:

To estimate HIV incidence using successive cross-sectional surveys by creating retrospective nested cohorts among MSM, people who inject drugs (PWID), and heterosexually active persons (HET).

Design:

Cohorts were created among participants who had at least one repeat observation across four surveillance cycles from National HIV Behavioral Surveillance in 20 US cities.

Methods:

Repeat participants were identified using a combination of date of birth, race/ethnicity, metropolitan statistical area, and gender. The analysis was limited to participants who tested negative for HIV at baseline and were assumed to be at risk between cycles. We calculated person-years at risk from the individual time between cycles and used the total number of seroconversions to estimate incidence and a Poisson distribution to approximate variance. Rate ratios were calculated using age, gender, race/ethnicity, and region.

Results:

From 2008 to 2019, successive surveys recaptured nested cohorts of 1747 MSM, 3708 PWID, and 1396 HET. We observed an incidence rate of 2.5 per 100 person-years [95% confidence interval (CI) 2.1–2.8) among MSM; 0.6 per 100 person-years (95% CI 0.5–0.7) among PWID; and 0.3 per 100 person-years (95% CI 0.1–0.4) among HET. HIV incidence was higher among younger MSM, black MSM (compared with white MSM), and PWID residing in the South and territories (compared with the Midwest).

Conclusion:

These estimates are consistent with previously published incidence estimates from prospective cohort studies among these populations. Using repeat cross-sectional surveys to simulate a cohort, may serve as another strategy in estimating HIV incidence.
Incidental Uptake in a Subacute Stroke on 18F-Piflufolastat PSMA PET/CT
Authors: Lewis Miles C. , Wale Daniel J. , Liao Eric , Viglianti Benjamin L.
Published: September 2023

Prostate-specific membrane antigen (PSMA) PET/CT has proven to be effective in the evaluation of prostate cancer and has become increasingly used clinically as multiple radiopharmaceuticals have become commercially available. With increasing use, incidental uptake from a variety of nononcologic processes will be encountered and considered interpretive pitfalls. We outline a case of a 71-year-old man who underwent imaging with PSMA PET/CT, which demonstrated uptake in the left parietal-temporal junction that was shown to be a subacute stroke. This case demonstrates a reported cause of uptake on PSMA PET for which the underlying mechanism is not yet well understood.
Thyroid Accumulation of 99mTc-DTPA in Graves Disease
Authors: Zhong Peng , Yang Jiahuan , Wang Yimiao , Wei Li , Chen Libo
Published: September 2023

99mTc-DTPA dynamic renal scintigraphy for evaluating glomerular filtration rate was performed in a 29-year-old woman with hyperuricemia and Graves disease. Subsequently, 99mTc-DTPA orbital scintigraphy was conducted to determine the activity of Graves ophthalmopathy. Thyroid accumulation of 99mTc-DTPA was incidentally identified. This should be cautiously distinguished from 99mTc-pertechnetate uptake, considering that the salivary glands, oral cavity, and stomach were not visualized. Our case demonstrates that augmentation of blood supply, enhancement of capillary permeability, and accumulation of inflammatory exudate may be involved in the pathological process of Graves disease.
Best Practice Guidelines for Ostomy Care in Neonates, Children, and Adolescents
Authors: Forest-Lalande Louise
Published: September 2023

Pediatric ostomy care nursing is primarily based on best practice principles; evidence supporting care remains sparse. Although many principles of ostomy care are similar across the life span, the indications for ostomy surgery and clinical approach differ when working with neonates, children, and adolescents. An international group of pediatric ostomy care experts was brought together to offer their expertise on caring for children with an ostomy. Best practice guidelines were developed based on literature review and consensus among expert panelists. The purpose of these guidelines is to provide a resource for best practices to health care professionals caring for pediatric patients with an ostomy. This article is divided into 2 sections: the first highlights clinical aspects of pediatric ostomy care, while the second addresses psychosocial aspects of ostomy care, including effects of an ostomy on the family. These guidelines address ostomy care and need within the full spectrum of the pediatric age groups, from neonates to adolescents.
Good Things Don't Always Come in Small Packages
Authors: Beitz Janice M. , Kennedy-Evans Karen Lou
Published: September 2023

The epidemic of obesity and morbid obesity is straining the American health care system's ability to provide quality patient care. Patients with Class 3 (also referred to as morbid or severe) obesity require specialized equipment, unique approaches in the delivery of care, and understanding of the biopsychosocial pathophysiologic mechanisms underlying their condition. This article defines Class 3 obesity, its pathophysiology, and discusses issues that arise when providing quality care of these individuals including safe patient handling, right-sized equipment, and empathetic interpersonal care. We also discuss skin and wound care issues associated with Class 3 obesity.
Patient Education in Intermittent Catheterization
Authors: Quallich Susanne , Lajiness Michelle , Engberg Sandra , Gray Mikel
Published: September 2023

Despite recent advances in intermittent catheter features, evidence guiding how to best educate patients when beginning and continuing a program of intermittent catheterization remains sparse. To address this gap and guide best practice, a scoping review was conducted and a consensus panel of clinicians and researchers with expertise in intermittent catheterization was convened in person during December 2022 in Austin, Texas, to develop evidence and consensus-based statements guiding instruction of patients beginning intermittent self or assisted catheterization. This article describes the 15 consensus-based statements that can be used to guide best practice in patient education on intermittent catheterization.
Comparing Rationale for Opioid Prescribing Decisions after Surgery with Subsequent Patient Consumption: A Survey of the Highest Quartile of Prescribers
Authors: Beaulieu-Jones Brendin R , Marwaha Jayson S , Kennedy Chris J , Le Danny , Berrigan Margaret T , Nathanson Larry A , Brat Gabriel A
Published: September 2023

Background:

Opioid prescribing patterns, including those after surgery, have been implicated as a significant contributor to the US opioid crisis. A plethora of interventions–from nudges to reminders–have been deployed to improve prescribing behavior, but reasons for persistent outlier behavior are often unknown.

Study Design:

Our institution employs multiple prescribing resources and a near real-time, feedback-based intervention to promote appropriate opioid prescribing. Since 2019, an automated system has emailed providers when a prescription exceeds the 75 th percentile of typical opioid consumption for a given procedure–as defined by institutional data collection. Emails include population consumption metrics and an optional survey on rationale for prescribing. Responses were analyzed to understand why providers choose to prescribe atypically large discharge opioid prescriptions. We then compared provider prescriptions against patient consumption.

Results:

During the study period, 10,672 eligible post-surgical patients were discharged. 2,013 prescriptions (29.4% of opioid prescriptions) exceeded our institutional guideline. Surveys were completed by outlier prescribers for 414 (20.6%) encounters. Among patients where both consumption data and prescribing rationale surveys were available, 35.2% did not consume any opioids after discharge and 21.5% consumed <50% of their prescription. Only 93 (39.9%) patients receiving outlier prescriptions were outlier consumers. Most common reasons for prescribing outlier amounts were attending preference (34%) and prescriber analysis of patient characteristics (34%).

Conclusions:

The top quartile of opioid prescriptions did not align with, and often far exceeded, patient post-discharge opioid consumption. Providers cite assessment of patient characteristics as a common driver of decision-making, but this did not align with patient usage for approximately 50% of patients.
No phylogenetic evidence for angiosperm mass extinction at the Cretaceous–Palaeogene (K-Pg) boundary
Authors: Thompson Jamie B. , Ramírez-Barahona Santiago
Published: September 2023

The Cretaceous–Palaeogene mass extinction event (K-Pg) witnessed upwards of 75% of animal species going extinct, most notably among these are the non-avian dinosaurs. A major question in macroevolution is whether this extinction event influenced the rise of flowering plants (angiosperms). The fossil record suggests that the K-Pg event had a strong regional impact on angiosperms with up to 75% species extinctions, but only had a minor impact on the extinction rates of major lineages (families and orders). Phylogenetic evidence for angiosperm extinction dynamics through time remains unexplored. By analysing two angiosperm mega-phylogenies containing approximately 32 000–73 000 extant species, here we show relatively constant extinction rates throughout geological time and no evidence for a mass extinction at the K-Pg boundary. Despite high species-level extinction observed in the fossil record, our results support the macroevolutionary resilience of angiosperms to the K-Pg mass extinction event via survival of higher lineages.
Understanding community level influences on the prevalence of SARS-CoV-2 infection in England: new insights from comparison over time and space
Authors: Joshi Chaitanya , Ali Arif , ÓConnor Thomas , Chen Li , Jahanshahi Kaveh
Published: September 2023

Understanding and monitoring the major influences on SARS-CoV-2 prevalence is essential to inform policy making and devise appropriate packages of non-pharmaceutical interventions. Through evaluating community level influences on the prevalence of SARS-CoV-2 infection and their spatio-temporal variations in England, this study aims to provide some insights into the most important risk parameters. We used spatial clusters developed in Jahanshahi and Jin (2021
Transportation
48
, 1329–1359 (doi:10.1007/s11116-020-10098-9)) as geographical areas with distinct land use and travel patterns. We also segmented our data by time periods to control for changes in policies or development of the disease over the course of the pandemic. We then used multivariate linear regression to identify influences driving infections within the clusters and to compare the variations of those between the clusters. Our findings demonstrate the key roles that workplace and commuting modes have had on some of the sections of the working population after accounting for several interrelated influences including mobility and vaccination. We found communities of workers in care homes and warehouses and to a lesser extent textile and ready meal industries and those who rely more on public transport for commuting tend to carry a higher risk of infection across all residential area types and time periods.
Metabolic rate does not explain performance on a short-term memory task or personality traits in juvenile chickens (
Gallus gallus domesticus
)
Authors: Watrobska Cecylia M. , Pasquier Grégoire , Leadbeater Ellouise , Portugal Steven J.
Published: September 2023

Metabolic rate determines life processes and the physiological requirements of an individual, and has recently been implicated as a driver of inter-individual variation in behaviour, with positive correlations associated with boldness, exploration and aggressive behaviours being recorded. While the link between metabolism and personality has been explored, little is known about the influence of metabolism on cognitive abilities. Here we used juvenile female chickens (
Gallus gallus domesticus
) to investigate the relationships between metabolic rate at rest, short-term memory, personality, and dominance. Resting metabolic rates of the chicks were measured over a three-week period, concurrently with measures of short-term memory using an analogue of the radial arm maze. We also measured latency to leave the shelter (boldness), neophobia (fear of novel objects) and dominance within a group, both before and after short-term memory trials. We found that metabolic rate did not explain inter-individual differences in short-term memory, personality traits or dominance, suggesting that energy allocated to these traits is independent of individual metabolic rate, and providing evidence for the independent energy-management hypothesis. Differences in short-term memory were also not explained by boldness or neophobia. Variation in behaviour in chicks, therefore, appears to be driven by separate, currently unknown variables.
Pronking and bounding allow a fast escape across a grassland populated by scattered obstacles
Authors: Righini Francesco , Carpineti Marina , Giavazzi Fabio , Vailati Alberto
Published: September 2023

Some quadrupeds have evolved the ability of pronking, which consists in leaping by extending the four limbs simultaneously. Pronking is typically observed in some ungulate species inhabiting grassland populated by obstacles such as shrubs, rocks and fallen branches scattered across the environment. Several possible explanations have been proposed for this peculiar behaviour, including the honest signalling of the fitness of the individual to predators or the transmission of a warning alert to conspecifics, but so far none of them has been advocated as conclusive. In this work, we investigate the kinematics of pronking on a two-dimensional landscape populated by randomly scattered obstacles. We show that when the density of obstacles is larger than a critical threshold, pronking becomes the gait that maximizes the probability of trespassing in the shortest possible time all the obstacles distributed across the distance fled, and thus represents an effective escape strategy based on a simple open-loop control. The transition between pronking and more conventional gaits such as trotting and galloping occurs at a threshold obstacle density and is continuous for a non-increasing monotone distribution of the height of obstacles, and discrete when the distribution is peaked at a non-zero height. We discuss the implications of our results for the autonomous robotic exploration on unstructured terrain.
Fluctuations in tissue growth portray homeostasis as a critical state and long-time non-Markovian cell proliferation as Markovian
Authors: Lavalle Natalia G. , Chara Osvaldo , Grigera Tomás S.
Published: September 2023

Tissue growth is an emerging phenomenon that results from the cell-level interplay between proliferation and apoptosis, which is crucial during embryonic development, tissue regeneration, as well as in pathological conditions such as cancer. In this theoretical article, we address the problem of stochasticity in tissue growth by first considering a minimal Markovian model of tissue size, quantified as the number of cells in a simulated tissue, subjected to both proliferation and apoptosis. We find two dynamic phases, growth and decay, separated by a critical state representing a homeostatic tissue. Since the main limitation of the Markovian model is its neglect of the cell cycle, we incorporated a refractory period that temporarily prevents proliferation immediately following cell division, as a minimal proxy for the cell cycle, and studied the model in the growth phase. Importantly, we obtained from this last model an effective Markovian rate, which accurately describes general trends of tissue size. This study shows that the dynamics of tissue growth can be theoretically conceptualized as a Markovian process where homeostasis is a critical state flanked by decay and growth phases. Notably, in the growing non-Markovian model, a Markovian-like growth process emerges at large time scales.
Optimal structures for focusing and energy accumulation: mathematical models and intuition
Authors: Cherkaev Andrej , Cherkaev Elena , Lurie Konstantin
Published: September 2023

Metamaterials and composite structures are able to manipulate waves and focus fields and currents in desirable directions. Designs based on spatial and temporal variation of material properties create structures forcing fluxes into specified parts of the domain or concentrating energy into arrays of progressively sharpening pulses. The paper discusses examples of focusing structures, mathematical and intuitive considerations that influence optimal design theory. The optimality requirement introduces zones of optimal composites with variable microgeometry. The observed absence of classical solutions motivates the extension of the class of optimal partitions to composites. Such materials also provide a solution to the problem of optimal design of a thermal lens focusing thermal fluxes when the incoming fluxes are not completely known in advance. An extension of designs to dynamical materials such as space–time checkerboard composites introduces metamaterials with additional capabilities that control the accumulation of energy in the propagating waves. The discussed mathematical methods of focusing and suitable properties alternation targeted on optimality are illustrated by physical examples.
Evidence for a reproductive sharing continuum in cooperatively breeding mammals and birds: consequences for comparative research
Authors: Ben Mocha Yitzchak , Dahan Tal , Zou Yuqi , Griesser Michael , Markman Shai
Published: September 2023

Extreme reproductive skew occurs when a dominant female/male almost monopolizes reproduction within a group of multiple sexually mature females/males, respectively. It is sometimes considered an additional, restrictive criterion to define cooperative breeding. However, datasets that use this restrictive definition to classify species as cooperative breeders systematically overestimate reproductive skew by including groups in which reproduction cannot be shared by definition (e.g. groups with a single female/male). Here, we review the extent of reproductive sharing in 41 mammal and 37 bird species previously classified as exhibiting alloparental care and extreme reproductive skew, while only considering multi-female or multi-male groups. We demonstrate that in groups where unequal reproduction sharing is possible, extreme reproductive skew occurs in a few species only (11/41 mammal species and 12/37 bird species). These results call for significant changes in datasets that classify species' caring and mating system. To facilitate these changes, we provide an updated dataset on reproductive sharing in 63 cooperatively breeding species. At the conceptual level, our findings suggest that reproductive skew should not be a defining criterion of cooperative breeding and support the definition of cooperative breeding as a care system in which alloparents provide systematic care to other group members’ offspring.
Collections of small urban parks consistently support higher species richness but not higher phylogenetic or functional diversity
Authors: La Sorte Frank A. , Clark Jeffrey A. G. , Lepczyk Christopher A. , Aronson Myla F. J.
Published: September 2023

When prioritizing regions for conservation protection, decisions are often based on the principle that a single large reserve should support more species than several small reserves of the same total area (SLOSS). This principle remains a central paradigm in conservation planning despite conflicting empirical evidence and methodological concerns. In urban areas where small parks tend to dominate and policies to promote biodiversity are becoming increasingly popular, determining the most appropriate prioritization method is critical. Here, we document the role of SLOSS in defining the seasonal diversity of birds in 475 parks in 21 US cities. Collections of small parks were consistently associated with higher species richness, spatial turnover and rarity. Collections of both small and large parks were associated with higher phylogenetic and functional diversity whose patterns varied across seasons and cities. Thus, collections of small parks are a reliable source of species richness driven by higher spatial turnover and rarity, whereas collections of both small and large parks contain the potential to support higher phylogenetic and functional diversity. The presence of strong intra-annual and geographical variation emphasizes the need for regional prioritization strategies, where multiple diversity metrics are examined across parks and seasons.
Sexual selection in seaweed? Testing Bateman's principles in the red algaGracilaria gracilis
Authors: Lavaut E. , Valero M. , Mauger S. , Guillemin M. L. , Destombe C. , Dufay M.
Published: September 2023

In anisogamous species, sexual selection is expected to be stronger in males. Bateman's principles state that the variance in (i) reproductive and (ii) mating success is greater for males, and (iii) the relationship between reproductive success and mating success (the Bateman gradient) is also stronger for males than for females. Sexual selection, based on Bateman's principles, has been demonstrated in animals and some angiosperms, but never in a seaweed. Here we focus on the oogamous haploid-diploid rhodophyteGracilaria gracilisin which previous studies have shown evidence for non-random mating, suggesting the existence of male–male competition and female choice. We estimated mating and reproductive success using paternity analyses in a natural population where up to 92% of fertilizations occurred between partners of that population. The results show that the variance in mating success is significantly greater in males than in females and that the Bateman gradient is positive only in males. Distance to female partners also explains a minor part of the variance in male mating success. Although there is no evidence for sexual dimorphism, our study supports the hypothesis that sexual selection occurs inG. gracilis, probably on male traits, even if we cannot observe, characterize or quantify them yet.
One year experience of Achromobacter bacteremia at a tertiary care hospital in Northern India
Authors: Kar Mitra , Singh Romya , Tejan Nidhi , Jamwal Ashima , Dubey Akanksha , Chaudhary Radhika , Sahu Chinmoy , Patel Sangram Singh , Kumari Pooja , Ghar Malay
Published: September 2023

Introduction.

Achromobacter

is a Gram-negative, motile, obligate aerobic and non-fermentative bacterium. It is an emerging pathogen in the hospital environment as it is frequently found in various solutions.

Hypothesis/Gap Statement. Information about the incidence and risk factors of

Achromobacter

bacteremia from India is limited.

Aim. We conducted this study to identify the risk factors and underlying conditions predisposing to bacteremia by

Achromobacter

spp. and analyse the antibiotic resistance pattern of the isolates.

Methodology. We performed a retrospective observational study where automated blood cultures positive for

Achromobacter

spp. were assessed for clinical characteristics and antibiotic susceptibility patterns from January 2022 to December 2022 in the microbiology laboratory of a tertiary care centre in Northern India.

Results. A total of 14 cases (14/2435, 0.57 %) of

Achromobacter

spp. were identified from bloodstream infections in one year. The mean age of the patients was 37.59±23.17 years with a male predominance (8/14, 57.1 %). All patients were managed on intravenous antibiotics and intravenous access as peripheral line catheters and only 5(5/14, 35.7 %) patients were managed on central line catheters. The isolates were found highly susceptible to ticarcillin-clavulanic acid (14/14, 100.0 %) followed by fluoroquinolones (12/14, 85.72 %) and trimethoprim-sulphamethoxazole (12/14, 85.72 %). Only 57.14 % (8/14, 57.14 %) of the patients were susceptible to piperacillin-tazobactam. The all-cause 40 day mortality was observed in 35.7 % (5/14, 35.7 %) with two deaths that were directly attributable to sepsis.

Conclusion. This study provides insight into the incidence of

Achromobacter

bacteremia at our centre and the necessary antibiotic therapy to combat it.
ICTV Virus Taxonomy Profile: Phenuiviridae 2023
Authors: Sasaya Takahide , Palacios Gustavo , Briese Thomas , Di Serio Francesco , Groschup Martin H. , Neriya Yutaro , Song Jin-Won , Tomitaka Yasuhiro
Published: September 2023

The family Phenuiviridae comprises viruses with 2–8 segments of negative-sense or ambisense RNA, comprising 8.1–25.1 kb in total. Virions are typically enveloped with spherical or pleomorphic morphology but can also be non-enveloped filaments. Phenuivirids infect animals including livestock and humans, birds, plants or fungi, as well as arthropods that serve as single hosts or act as biological vectors for transmission to animals or plants. Phenuivirids include important pathogens of humans, livestock, seafood and agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Phenuiviridae, which is available at ictv.global/report/phenuiviridae.
Repression of the major immediate early promoter of human cytomegalovirus allows transcription from an alternate promoter
Authors: Mason Rebecca , Bradley Eleanor , Wills Mark , Sinclair John , Reeves Matthew
Published: September 2023

Following infection, the human cytomegalovirus (HCMV) genome becomes rapidly associated with host histones which can contribute to the regulation of viral gene expression. This can be seen clearly during HCMV latency where silencing of the major immediate early promoter (MIEP), normally responsible for expression of the key lytic proteins IE72 and IE86, is mediated by histone methylation and recruitment of heterochromatin protein 1. Crucially, reversal of these histone modifications coupled with histone acetylation drives viral reactivation which can be blocked with specific histone acetyltransferase inhibitors (HATi). In lytic infection, a role for HATi is less clear despite the well-established enhancement of viral replication observed with histone deacetylase inhibitors. Here we report that a number of different broad-acting HATi have a minor impact on viral infection and replication during lytic infection with the more overt phenotypes observed at lower multiplicities of infection. However, specific analyses of the regulation of major immediate early (MIE) gene expression reveal that the HATi C646, which targets p300/CBP, transiently repressed MIE gene expression via inhibition of the MIEP but by 24 h post-infection MIE gene expression was rescued due to compensatory activation of an alternative IE promoter, ip2. This suggested that silencing of the MIEP promoted alternative ip2 promoter activity in lytic infection and, consistent with this, ip2 transcription is impaired in cells infected with a recombinant HCMV that does not auto-repress the MIEP at late times of infection. Furthermore, inhibition of the histone methyltransferases known to be responsible for auto-repression is similarly inhibitory to ip2 transcription in wild-type infected cells. We also observe that these discrete transcriptional activities of the MIEP and ip2 promoter are also reflected in reactivation; essentially in cells where the MIEP is silenced, ip2 activity is easier to detect at very early times post-reactivation whereas in cells where robust activation of the MIEP is observed ip2 transcription is reduced or delayed. Finally, we observe that inhibition of pathways demonstrated to be important for reactivation of HCMV in dendritic cells, e.g. in response to IL-6, are preferentially important for activation of the MIEP and not the ip2 promoter. Together, these data add to the hypothesis that the existence of multiple promoters within the MIE region of HCMV can drive reactivation in a cell type- and ligand-specific manner and also suggest that inter-dependent regulatory activity between the two promoters exists.
BBSdb, an open resource for bacterial biofilm-associated proteins
Authors: Zhang Zhiyuan , Pan Yuanyuan , Hussain Wajid , Li Qingqing , Li Erguang
Published: September 2023

Bacterial biofilms are organized heterogeneous assemblages of microbial cells encased within a self-produced matrix of exopolysaccharides, extracellular DNA and proteins. Over the last decade, more and more biofilm-associated proteins have been discovered and investigated. Furthermore, omics techniques such as transcriptomes, proteomes also play important roles in identifying new biofilm-associated genes or proteins. However, those important data have been uploaded separately to various databases, which creates obstacles for biofilm researchers to have a comprehensive access to these data. In this work, we constructed BBSdb, a state-of-the-art open resource of bacterial biofilm-associated protein. It includes 48 different bacteria species, 105 transcriptome datasets, 21 proteome datasets, 1205 experimental samples, 57,823 differentially expressed genes (DEGs), 13,605 differentially expressed proteins (DEPs), 1,930 ‘Top 5% differentially expressed genes’ and a predictor for prediction of biofilm-associated protein. In addition, 1,781 biofilm-associated proteins, including annotation and sequences, were extracted from 942 articles and public databases via text-mining analysis. We usedE. colias an example to represent how to explore potential biofilm-associated proteins in bacteria. We believe that this study will be of broad interest to researchers in field of bacteria, especially biofilms, which are involved in bacterial growth, pathogenicity, and drug resistance.

Availability and implementation

The BBSdb is freely available athttp://124.222.145.44/#!/.
Parallel loss of sex in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
Authors: Hoshino Masakazu , Cossard Guillaume , Haas Fabian B. , Kane Emma I. , Kogame Kazuhiro , Jomori Takahiro , Wakimoto Toshiyuki , Coelho Susana M.
Published: September 2023

Abstract

Sexual reproduction is widespread among eukaryotes, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of taxa. Despite extensive research on the evolution of asexuality from sexual ancestors, the molecular changes underpinning the switch to asexual reproduction remain elusive, particularly in organisms with haploid sexual systems such as bryophytes, and red and brown algae in which males and females are haploid and multicellular. Here, we investigate independent events in which asexuality has emerged from sexual ancestor lineages in species of the brown algalScytosiphon, we examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that individuals from asexual, female-only (‘Amazon’) populations lose their ability to produce and sex pheromone and, consequently, are unable to attract and fuse with male gametes, whereas they gain the ability to trigger parthenogenic (asexual) development from large, unfertilized eggs. This independent and convergent decline in pheromone production and optimization of asexual traits is accompanied by convergent changes in gene expression, including de-feminization and masculinization of the Amazon gamete transcriptomes. These data are consistent with the idea that decay of female functions, rather than relaxation of sexual antagonism, is the dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we identify a locus on an autosomal protein-coding gene that is associated with the switch to asexuality. We propose that the sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.
Dynamic Inference by Model Reduction
Authors: Priorelli Matteo , Stoianov Ivilin Peev
Published: September 2023

Abstract

How do we infer which one of several targets another agent is following? And how are we capable of grasping an object on the fly? Reducing a model as complex as the surrounding dynamic environment into a small set of simpler hypotheses is a reasonable cognitive solution, but how can the brain compare and choose among dynamic hypotheses? Recent advances in Bayesian Model Reduction have led to innovative solutions to actively infer the state of affairs of the world and perform discrete planning with continuous signals, but dealing with highly dynamic contexts is a difficult matter. We propose that choosing among flexible hypotheses is possible by using reduced priors sampled from the dynamics of a generative model. Each reduced prior corresponds to an alternative future world constantly generated from the current observations, which the agent can use to accumulate evidence for a discrete hypothesis. We tested the approach on two everyday tasks: inferring a dynamic trajectory and grasping a moving object, which the model solved with high accuracy. Our study may thus shed light on how agents can smoothly generate and infer static intentions that result in dynamic behaviors, and on the specific role of intention precisions in motor learning.
A comparison of telencephalon composition among chickens, junglefowl, and wild galliforms
Authors: Racicot Kelsey J. , Ham Jackson R. , Augustine Jacqueline , Henriksen Rie , Wright Dominic , Iwaniuk Andrew N.
Published: September 2023

Domestication is the process of modifying animals for human benefit through selective breeding in captivity. One of the traits that often diverges is the size of the brain and its constituent regions; almost all domesticated species have relatively smaller brains and brain regions than their wild ancestors. Although the effects of domestication on the brain have been investigated across a range of both mammal and bird species, almost nothing is known about the neuroanatomical effects of domestication on the world’s most common bird: the chicken (Gallus gallus). We compared the quantitative neuroanatomy of the telencephalon of white leghorn chickens with red junglefowl, their wild counterpart, and several wild galliform species. We focused specifically on the telencephalon because telencephalic regions typically exhibit the biggest differences in size in domesticate-wild comparisons. Relative telencephalon size was larger in chickens than in junglefowl and ruffed grouse (Bonasa umbellus). The relative size of telencephalic regions did not differ between chickens and junglefowl but did differ in comparison with ruffed grouse. Ruffed grouse had larger hyperpallia and smaller entopallial, nidopallial and striatal volumes than chickens and junglefowl. Multivariate analyses that included an additional three wild grouse species corroborated these findings: chicken and junglefowl have relatively larger nidopallial and striatal volumes than grouse. Conversely, the mesopallial and hyperpallial volumes tended to be relatively smaller in chickens and junglefowl. From this suite of comparisons, we conclude that chickens do not follow a pattern of widespread decreases in telencephalic region sizes that is often viewed as typical of domestication. Instead, chickens have undergone a mosaic of changes with some regions increasing and others decreasing in size and there are few differences between chickens and junglefowl.
Comparative Analysis of Association Networks Using Single-Cell RNA Sequencing Data Reveals Perturbation-Relevant Gene Signatures
Authors: Nouri Nima , Gaglia Giorgio , Mattoo Hamid , Rinaldis Emanuele de , Savova Virginia
Published: September 2023

Single-cell RNA sequencing (scRNA-seq) data has elevated our understanding of systemic perturbations to organismal physiology at the individual cell level. However, despite the rich information content of scRNA-seq data, the relevance of genes to a perturbation is still commonly assessed through differential expression analysis. This approach provides a one-dimensional perspective of the transcriptomic landscape, risking the oversight of tightly controlled genes characterized by modest changes in expression but with profound downstream effects. We present GENIX (Gene Expression Network Importance eXamination), a novel platform for constructing gene association networks, equipped with an innovative network-based comparative model to uncover condition-relevant genes. To demonstrate the effectiveness of GENIX, we analyze influenza vaccine-induced immune responses in peripheral blood mononuclear cells (PBMCs) collected from recovered COVID-19 patients, shedding light on the mechanistic underpinnings of gender differences. Our methodology offers a promising avenue to identify genes relevant to perturbation responses in biological systems, expanding the scope of response signature discovery beyond differential gene expression analysis.

HIGHLIGHTS

Conventional methods used to identify perturbation-relevant genes in scRNA-seq data rely on differential expression analysis, susceptible to overlooking essential genes.

GENIX leverages cell-type-specific inferred gene association networks to identify condition-relevant genes and gene programs, irrespective of their specific expression alterations.

GENIX provides insight into the gene-regulatory response to the influenza vaccine in naïve and recovered COVID-19 patients, expanding on previously observed gender-specific differences.

GRAPHICAL ABSTRACT