bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acquisition of Borrelia burgdorferi sensu stricto (Spirochaetales: Spirochaetaceae) by Haemaphysalis longicornis (Acari: Ixodidae) nymphs during interrupted feeding
Authors: Parise Christina M , Ford Shelby L , Burtis James , Hojgaard Andrias , Eisen Rebecca J , Eisen Lars 
Published: January 2025

Abstract
A previous laboratory study using Haemaphysalis longicornis Neumann (Acari: Ixodidae) ticks of North American origin showed that larvae could acquire the Lyme disease spirochete, Borrelia burgdorferi sensu stricto (s.s.) (Spirochaetales: Spirochaetaceae) while feeding to completion on infected mice. However, the infection was lost during the molt to the nymphal stage. Nonetheless, questing H. longicornis nymphs and adults collected by drag sampling in the northeastern United States have been reported infected with B. burgdorferi s.s. DNA; occasionally these ticks appeared to be partially engorged. This raises the question of whether H. longicornis ticks can (i) acquire B. burgdorferi s.s. during an interrupted, partial blood meal on an infected host and (ii) transmit spirochetes while completing the blood meal on a second host. In this laboratory study, we demonstrated that H. longicornis nymphs could acquire B. burgdorferi s.s. from infected Mus musculus mice during a partial blood meal. Borrelia burgdorferi s.s. was detected by a multiplex polymerase chain reaction amplicon sequencing assay in 2 of 32 (6.3%) nymphs allowed to remain attached to infected mice for 48 h but, paradoxically, not in any of 25 nymphs that remained attached to infected mice for 72 h. Unfortunately, due to the low percentage of infected nymphs, we were not able to examine if such partially fed, infected nymphs were able to transmit B. burgdorferi s.s. while completing their blood meal on a second, naïve host.
Integrative taxonomy of new neritimorph limpets from Indian Ocean deep-sea hot vents shed light on their biogeographic history
Authors: Gu Xinyu , Chen Chong , Gao Kexin , Zhou Yadong , Sun Jin 
Published: January 2025

Abstract
Red-blooded neritimorph gastropods in the subfamily Shinkailepadinae are specialists of chemosynthesis-based ecosystems, with the most diverse genus Shinkailepas endemic to deep-sea hydrothermal vents. All described Shinkailepas species have so far been from the western Pacific, despite reports of unidentified Shinkailepas from the Indian Ocean in the literature for decades. Here, we use an integrative approach to characterize and describe these Indian Ocean vent neritimorphs for the first time, based on material collected from the Carlsberg Ridge (CR) and the Central Indian Ridge (CIR). We name two new species: Shinkailepas tiarasimia sp. nov. from both the CR and the CIR, and Shinkailepas cornuthauma sp. nov. from the CR. A combination of shell and epipodial lobe characters reliably separate these new species from their described congeners. A phylogenetic reconstruction of all known Shinkailepas species using 658 bp of the mitochondrial COI gene reveal two separate major clades within the genus, each with an Indian Ocean species—implying two independent colonizations of Indian Ocean vents by separate lineages. Our finding of two new species on the CR, including one not known anywhere else, underscores the unique biodiversity at these vents and strengthens the case for protecting them from potential deep-sea mining activities.
Trends in Antepartum, Delivery, and Postpartum Venous Thromboembolism
Authors: Kola Olivia , Huang Yongmei , D’Alton Mary E. , Wright Jason D. , Friedman Alexander M. 
Published: January 2025

OBJECTIVE:
To assess trends in risk for obstetric venous thromboembolism (VTE).

METHODS:
This retrospective cohort study analyzed data from the 2008–2019 Merative MarketScan Commercial Claims and Encounters and Medicaid Multi-State databases. Women aged 15–54 years with a delivery hospitalization and health care enrollment from 1 year before pregnancy to 60 days after delivery were identified. Risk for VTE during pregnancy from 2009 to 2019 was analyzed with joinpoint regression, with trends reported as the average annual percent change (APC). Venous thromboembolism events were identified with diagnosis codes along with pharmacy receipt of anticoagulants. Additionally, the association between risk factors for VTE and VTE events was evaluated with log-Poisson regression models with unadjusted and adjusted risk ratios (aRR) with 95% CIs as measures of association.

RESULTS:
Among 1,970,971 pregnancies, there were 5,270 VTE events, of which 35.5% (n=1,871) included a pulmonary embolism diagnosis and 64.5% (3,399) included a deep vein thrombosis diagnosis, alone. Risk for VTE increased significantly during pregnancy over the study period, with an APC of 9.2% (95% CI, 5.7–12.9%). Rates of VTE also increased individually during the antenatal period (APC 8.2%, 95% CI, 3.7–12.9%), during delivery hospitalizations (APC 12.2%, 95% CI, 7.4–17.3%), during the postpartum period (APC 8.4%, 95% CI, 5.9–11.0%), and individually for vaginal and cesarean delivery hospitalizations. Trends analyses individually for pulmonary embolism (APC 12.4%, 95% CI, 8.6–16.4%) and deep vein thrombosis (APC 7.6%, 95% CI, 4.0–11.3%) also demonstrated significant increases. In adjusted analyses for VTE, obesity (aRR 1.91, 95% CI, 1.78–2.05), chronic heart disease (aRR 3.14, 95% CI, 2.93–3.37), tobacco use (aRR 1.61, 95% CI, 1.34–1.95), asthma (aRR 1.46, 95% CI, 1.33–1.60), and preeclampsia (aRR 1.44, 95% CI, 1.31–1.58) were the factors associated the greatest increased adjusted relative risk.

CONCLUSION:
Risk for obstetric VTE increased significantly over the study period. Risk increased during the antenatal, delivery, and postpartum periods and for both cesarean and vaginal delivery.
Rise in Minimally Invasive Surgery for Colorectal Cancer Is Associated With Adoption of Robotic Surgery
Authors: Manisundaram Naveen , Childers Christopher P. , Hu Chung-Yuan , Uppal Abhineet , Konishi Tsuyoshi , Bednarski Brian , White Michael G , Peacock Oliver , You Y. Nancy , Chang George J. 
Published: January 2025

BACKGROUND:
Minimally invasive surgery is associated with improved short-term outcomes and similar long-term oncologic outcomes for colorectal cancer patients compared with open surgery. Although the robotic approach has ergonomic and technical benefits, how it has impacted utilization of traditional laparoscopic surgery and minimally invasive surgery overall is unclear.

OBJECTIVE:
Describe trends in open, robotic, and laparoscopic approaches for colorectal cancer resections and examine factors associated with minimally invasive surgery.

DESIGN:
Retrospective cohort study using data from the National Cancer Database from 2010 through 2020.

SETTING:
Commission on Cancer-accredited U.S. facilities.

PATIENTS:
Patients diagnosed with nonmetastatic colon or rectal adenocarcinoma.

MAIN OUTCOMES MEASURES:
Surgical approach rates (open, robotic, laparoscopic).

RESULTS:
We identified 475,001 patients diagnosed with nonmetastatic colorectal adenocarcinoma, of whom 192,237 (40.5%) underwent open surgery, 64,945 (13.7%) underwent robotic surgery, and 217,819 (45.9%) underwent laparoscopic surgery. For colon cancer, laparoscopic minimally invasive surgery use steadily increased, with a peak prevalence of 54.0% in 2016, and total minimally invasive surgery (robotic + laparoscopic) was performed more often than open surgery from 2013 through 2020. For rectal cancer, laparoscopic minimally invasive surgery had a peak prevalence of 37.2% in 2014 and declined from 2014 through 2020; robotic surgery prevalence increased throughout the study period (5.5% in 2010, 24.7% in 2015, 48.8% in 2020). Minimally invasive surgery use increased in facilities performing robotic surgery every year during the study period. For both colon and rectal cancer, use of open surgery decreased across all facilities throughout the study period.

LIMITATIONS:
Utilized National Cancer Database which may not be generalizable to non-Commission on Cancer institutions.

CONCLUSIONS:
Minimally invasive surgery steadily increased across all facilities from 2010 through 2020. Open resections declined, laparoscopic resections plateaued, and robotic resections increased for colon and rectal cancer. Minimally invasive surgery increases may be driven by increases in robot-assisted surgery. See Video Abstract.
Management of psoriasis in women 18 to 45 years of age in Australia and Japan: insights from patient and dermatologist surveys
Authors: Yamaguchi Yukie , Spelman Lynda , Mizutani Yoko , Lukowski Bartosz , Lanzafame Alfred , Smith Annika 
Published: January 2025

Background:
A psoriasis (PSO) diagnosis may pose specific treatment challenges for women of childbearing age (WoCBA) who are considering pregnancy, are pregnant, or have just given birth.

Objective:
To report perspectives of WoCBA with PSO regarding pregnancy and dermatologists about the disease management of these women in Australia and Japan.

Methods:
Online surveys were completed by women aged 18 to 45 years who were pregnant within the past 5 years with moderate to severe PSO and dermatologists.

Results:
In Japan (n = 31) and Australia (n = 27), most WoCBA with PSO did not feel adequately informed about pregnancy planning and had concerns regarding the safety of tumor necrosis factor inhibitors (TNFi) when used during pregnancy. Dermatologists (Australia: n = 40; Japan: n = 97) also had safety concerns around prescribing TNFi during pregnancy, and most were impartial toward or not at all comfortable with prescribing TNFi to women who were pregnant or actively planning pregnancy. Dermatologists felt that more safety data on pregnancy, lactation, and pediatric outcomes 5 years postdelivery would increase their comfort with prescribing TNFi.

Limitations:
Limitations included small respondent size, a lack of formal validation for questionnaires, recall bias among participants, and generalizability of results to all WoCBA with PSO. Response rates of survey participants were also not collected.

Conclusion:
Additional safety information can help address concerns about biologic use (including TNFi) in WoCBA, enabling dermatologists to make informed treatment recommendations in such patients.
Global perspectives on transplant disparities
Authors: Brosi Deena , Wainstein Marina , Cervantes Lilia , Schold Jesse D. 
Published: January 2025

Purpose of review
Our goal was to review and summarize the current state of global disease burden from organ failure and the efforts to improve outcomes with organ transplantation. We also reviewed intra- and inter-country disparities in organ failure and organ transplantation along with potential mechanisms to improve access to organ transplantation globally.

Recent findings
Many disparities and inequities observed globally can be characterized by the country's income category. Low- and lower-middle income countries (LLMICs) have higher rates of communicable disease-attributed organ failure, while upper-income countries (UICs) have high overall prevalence due to global growth in noncommunicable etiologies of organ failure. Many downstream disparities in access to organ transplantation and outcomes are associated with country income designation. Improvements in data collection and surveillance of populations with organ failure and organ transplantation are urgently needed.

Summary
Improving outcomes for patients with end-organ disease globally will require countries to improve organ transplantation access and care. For LLMICs, collaboration with international transplant systems and engagement with neighboring countries may establish important foundations for organ transplant systems. For UICs, increasing organ donor availability through technological advances and increasing public engagement will help meet the growing needs for organ transplantation as an important treatment modality.
The Postmortem Pathology of Sudden Death in Chronic Alcohol Exposure and Acute Alcohol Intoxication
Authors: Haynes Harry R. , Gallagher Patrick J. , Thom Maria H. , Morovat Reza A. , Delaney Russell J. , Jeffery Amanda J. 
Published: January 2025

Abstract
Chronic alcohol exposure is common in all societies and is seen at high rates during coronial (medicolegal) postmortem examinations. In both setting of acute alcohol intoxication and chronic misuse, a wide range of pathologies and mechanisms of death may be encountered, particularly with regard to sudden, unexpected or violent deaths. These warrant special attention. In this review, we examine the approach to postmortem examination where alcohol is likely to have played a key role in death. Attention is given to the scene of death, patterns of traumatic injury, systemic pathology (particularly of chronic alcohol exposure), seizures related to alcohol, and appropriate biochemical investigations.
PhyloMix: Enhancing microbiome-trait association prediction through
phylogeny-mixing augmentation
Authors: Jiang Yifan , Liao Disen , Zhu Qiyun , Lu Yang Young 
Published: January 2025

Abstract

Motivation
Understanding the associations between traits and microbial composition
is a fundamental objective in microbiome research. Recently, researchers
have turned to machine learning (ML) models to achieve this goal with
promising results. However, the effectiveness of advanced ML models is often
limited by the unique characteristics of microbiome data, which are
typically high-dimensional, compositional, and imbalanced. These
characteristics can hinder the models’ ability to fully explore the
relationships among taxa in predictive analyses. To address this challenge,
data augmentation has become crucial. It involves generating synthetic
samples with artificial labels based on existing data and incorporating
these samples into the training set to improve ML model
performance.

Results
Here we propose PhyloMix, a novel data augmentation method specifically
designed for microbiome data to enhance predictive analyses. PhyloMix
leverages the phylogenetic relationships among microbiome taxa as an
informative prior to guide the generation of synthetic microbial samples.
Leveraging phylogeny, PhyloMix creates new samples by removing a subtree
from one sample and combining it with the corresponding subtree from another
sample. Notably, PhyloMix is designed to address the compositional nature of
microbiome data, effectively handling both raw counts and relative
abundances. This approach introduces sufficient diversity into the augmented
samples, leading to improved predictive performance. We empirically
evaluated PhyloMix on six real microbiome datasets across five commonly used
ML models. PhyloMix significantly outperforms distinct baseline methods
including sample-mixing-based data augmentation techniques like vanilla
mixup and compositional cutmix, as well as the phylogeny-based method TADA.
We also demonstrated the wide applicability of PhyloMix in both supervised
learning and contrastive representation learning.

Availability
The Apache licensed source code is available at (https://github.com/batmen-lab/phylomix).
Discrimination of inherent characteristics of susceptible and resistant
strains ofAnopheles gambiaeby explainable Artificial Intelligence
Analysis of Flight Trajectories
Authors: Qureshi Yasser M. , Voloshin Vitaly , Gleave Katherine , Ranson Hilary , McCall Philip J. , Towers Cathy E. , Covington James A. , Towers David P. 
Published: January 2025

Abstract
Understanding mosquito behaviours is vital for development of
insecticide-treated bednets (ITNs), which have been successfully deployed in
sub-Saharan Africa to reduce disease transmission, particularly malaria.
However, rising insecticide resistance (IR) among mosquito populations, owing to
genetic and behavioural changes, poses a significant challenge. We present a
machine learning pipeline that successfully distinguishes between IR and
insecticide-susceptible (IS) mosquito behaviours by analysing trajectory data.
Data driven methods are introduced to accommodate common tracking system
shortcomings that occur due to mosquito positions being occluded by the bednet
or other objects. Trajectories, obtained from room-scale tracking of two IR and
two IS strains around a human-baited, untreated bednet, were analysed using
features such as velocity, acceleration, and geometric descriptors. Using these
features, an XGBoost model achieved a balanced accuracy of 0.743 and a ROC AUC
of 0.813 in classifying IR from IS mosquitoes. SHAP analysis helped decipher
that IR mosquitoes tend to fly slower with more directed flight paths and lower
variability than IS—traits that are likely a fitness advantage by enhancing
their ability to respond more quickly to bloodmeal cues. This approach provides
valuable insights based on flight behaviour that can reveal the action of
interventions and insecticides on mosquito physiology.
Mapping Global Causal Responses to Noninvasive Modulation of Genetically and
Spatially Targeted Neural Populations with Sonogenetic-fPET
Authors: Yang Yaoheng , Weixel Charlotte , Hu Zhongtao , Yue Yimei , Wang Isaac , Xu Lu , Chen Hong 
Published: January 2025

Abstract
Despite significant progress in brain circuit mapping over recent decades, a
major challenge remains: no method currently allows for the noninvasive
modulation of genetically and spatially defined neural populations while
simultaneously monitoring their global effects throughout the brain and body.
Here, we present sonogenetic-fPET, a technique that integrates sonogenetics with
[18F]-2-fluoro-2-deoxy-D-glucose functional positron
emission tomography (FDG-fPET) to overcome this challenge. Sonogenetics enables
noninvasive, spatially targeted modulation of neurons genetically engineered to
express the ultrasound-sensitive ion channel TRPV1, while FDG-fPET captures
glucose metabolic changes triggered by this stimulation across the brain and
body. We demonstrate the effectiveness of this technique by targeting neurons in
the dorsal striatum, showcasing its capability to map global network responses
to specific neuronal activation. Incorporating an acoustic hologram for
sonogenetics further enables flexible modulation of different brain regions
within a single mouse while concurrently mapping the resulting network activity.
In summary, sonogenetic-fPET offers a tool for dissecting the global responses
of the brain and body to the noninvasive modulation of genetically and spatially
defined neuronal populations.
Habitat quality influences gut microbiota via cortisol in Siberian flying
squirrels (Pteromys volans)
Authors: Petrullo Lauren , Santangeli Andrea , Wistbacka Ralf , Husby Arild , Raulo Aura 
Published: January 2025

ABSTRACT
Interactions between the mammalian neuroendocrine system and the gut
microbiota (i.e., the gut-brain axis) can shape how animals cope with
environmental challenges. For example, both immune function and the extraction
of energy from dietary items depend on microbiota, which can be influenced by
the environment directly through transmission or indirectly through
neuroendocrine responses. Environmental variation has been shown to translate
into variation in microbiome profiles among wild animals, but whether this is
due to different environmental microbial transmission or environmental
conditions evoking microbiome-modulating physiological stress responses is not
known. Here, we investigate covariation among habitat quality, cortisol levels
and gut microbiota in adult and juvenile Siberian flying squirrels
(Pteromys volans) inhabiting a region impacted by
variable rates of human disturbance. We test competing hypotheses related to
direct (e.g., via diet or transmission) versus indirect (e.g., via the gut-brain
axis) effects of habitat on the gut microbiota. Overall, we found that adults
had richer gut microbiota and higher concentrations of hair cortisol than
juveniles. Our measures of habitat quality exerted direct effects on cortisol
concentrations, but had no direct effects on microbiota. Regardless, cortisol
predicted microbiota composition among adult squirrels. Finally, structural
equation modeling revealed indirect effects of habitat quality on microbial
diversity by way of elevations in cortisol among adults. In contrast, among
juveniles, habitat-related cortisol variation had no downstream effects on
microbial diversity. Together, these findings provide evidence for indirect
effects of environmental quality on gut microbiota via the host endocrine
system, and suggest these effects can be age-dependent.
Ecological resource competition as a driver of metallome evolution
Authors: Sobol Morgan S. , Rucker Holly R. , Libby Eric , Kaçar Betül , Anbar Ariel D. 
Published: January 2025

Abstract
Undoubtedly, Earth’s first redox revolution, which culminated ∼2.4 billion
years ago in the Great Oxidation Event (GOE), fundamentally altered the
resources available to microbial communities, leading to novel ecological
competitions and evolutionary innovations. These eco-evolutionary dynamics are
largely unexplored, particularly at the molecular level. Here, we hypothesize
that such dynamics in the wake of the GOE explain the otherwise paradoxical
evolutionary history of metal use in nitrogen fixation by nitrogenase. This
ancient metalloenzyme exists in three isozymes, with distinct metal cofactors.
Recent research demonstrates that the most ancient isozyme, emerging a billion
years or more before the GOE, required a molybdenum (Mo)-based cofactor.
“Alternative” nitrogenases using iron (Fe) or vanadium (V) cofactors evolved
after the GOE. This history is puzzling because Mo availability in the
environmentincreasedafter the GOE, while Fe
availabilitydecreased, due to the contrasting
environmental redox behaviors of these elements. Why, then, did the alternatives
emerge only after the GOE? Using a simple model constrained by known microbial
Mo quotas, we demonstrate that a strong selection pressure for use of metals in
nitrogenase other than Mo is a likely consequence of competition between
nitrogen-fixing prokaryotes and nitrate-reducing microbes, which require Mo for
nitrate reduction and assimilation. This competition would have intensified
after the GOE due to increasing environmental availability of nitrate,
explaining the evolutionary timing of the nitrogenase isozymes. Ecological
resource competition therefore emerges as a third driver of metallome evolution
in deep-time, alongside the relative environmental availabilities and adaptive
advantages of particular metals.

Significance statement
The selection of metals in biochemical evolution is widely attributed to
either the relative environmental availability of specific metals or their
functional benefits in biological systems. We propose a third pressure,
ecological resource competition, which is typically overlooked as a driver
of molecular novelty in deep time. Specifically, we hypothesize that
competition between Mo-dependent nitrogen-fixing prokaryotes and
Mo-dependent nitrate reducers led to the emergence of Mo-free “alternative”
nitrogenase enzymes during the early Proterozoic. This novel hypothesis
explains the paradoxical emergence of alternative nitrogenases after the
Great Oxidation Event despite increasing ocean Mo abundances at that time.
Competition among microbial species for the same metals likely drove
molecular innovations, especially in response to dynamically changing
geochemical landscapes.