bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-symmetric responses of leaf onset date to natural warming and cooling in northern ecosystems
Authors: He Lei , Wang Jian , Ciais Philippe , Ballantyne Ashley , Yu Kailiang , Zhang Wenxin , Xiao Jingfeng , Ritter François , Liu Zhihua , Wang Xufeng , Li Xiaojun , Peng Shouzhang , Ma Changhui , Zhou Chenghu , Li Zhao-Liang , Xie Yaowen , Ye Jian-Sheng 
Published: September 2023

Abstract
The northern hemisphere has experienced regional cooling, especially during the global warming hiatus (1998–2012) due to ocean energy redistribution. However, the lack of studies about the natural cooling effects hampers our understanding of vegetation responses to climate change. Using 15,125 ground phenological time series at 3,620 sites since the 1950s and 31-year satellite greenness observations (1982–2012) covering the warming hiatus period, we show a stronger response of leaf onset date (LOD) to natural cooling than to warming, i.e. the delay of LOD caused by 1°C cooling is larger than the advance of LOD with 1°C warming. This might be because cooling leads to larger chilling accumulation and heating requirements for leaf onset, but this non-symmetric LOD response is partially offset by warming-related drying. Moreover, spring greening magnitude, in terms of satellite-based greenness and productivity, is more sensitive to LOD changes in the warming area than in the cooling. These results highlight the importance of considering non-symmetric responses of spring greening to warming and cooling when predicting vegetation-climate feedbacks.
Eviction and Poverty in American Cities
Authors: Collinson Robert , Humphries John Eric , Mader Nicholas , Reed Davin , Tannenbaum Daniel , van Dijk Winnie 
Published: September 2023

Abstract
More than two million U.S. households have an eviction case filed against them each year. Policy makers at the federal, state, and local levels are increasingly pursuing policies to reduce the number of evictions, citing harm to tenants and high public expenditures related to homelessness. We study the consequences of eviction for tenants using newly linked administrative data from two major urban areas: Cook County (which includes Chicago) and New York City. We document that before housing court, tenants experience declines in earnings and employment and increases in financial distress and hospital visits. These pre trends pose a challenge for disentangling correlation and causation. To address this problem, we use an instrumental variables approach based on cases randomly assigned to judges of varying leniency. We find that an eviction order increases homelessness and hospital visits and reduces earnings, durable goods consumption, and access to credit in the first two years. Effects on housing and labor market outcomes are driven by effects for female and Black tenants. In the longer run, eviction increases indebtedness and reduces credit scores.
Do the features of juvenile psoriatic arthritis change according to age? A comprehensive evaluation of the PeRA Research Group Registry
Authors: Karadağ Şerife Gül , Coskuner Taner , Demirkan Fatma Gül , Sonmez Hafize Emine , Ozdel Semanur , Çakan Mustafa , Otar Yener Gulcin , Ozturk Kubra , Demir Ferhat , Sozeri Betül , Aktay Ayaz Nuray 
Published: September 2023

Abstract

Objectives
To describe the clinical features and treatment outcomes of children with juvenile psoriatic arthritis (JPsA) and compare the distinct patterns of the disease between early-onset and late-onset age groups.

Methods
Patients with JPsA followed regularly for at least 6 months between 2010 and 2020 in seven paediatric rheumatology centres in Turkey were included in the study. The demographic features, clinical manifestations, treatment strategies and outcomes of the patients were evaluated retrospectively.

Results
A total of 87 (46 male/41 female) patients were included in the study. The mean age at diagnosis was 11.9 years (s.d. 4.5). Fifty-seven (65.5%) patients had psoriasis at the time of diagnosis and arthritis preceded psoriasis in 10 (11.5%) patients. Thirty (34.5%) patients had dactylitis, 28 (32.2%) had nail pitting, 36 (41.4%) had involvement of the small joints and 20 (23%) had enthesitis. Sacroiliitis was detected in 11 (12.6%) patients by MRI. ANA was positive in 35 (40.2%) patients. Twelve children (13.8%) were in the early-onset (&lt;5 years) group. Uveitis and ANA positivity were more common in the early-onset group. Active joint counts and activity scores of our patients showed significant improvement at month 6 and at the last control compared with baseline.

Conclusion
About one-third of patients with JPsA do not have psoriasis at the time of diagnosis. In some patients, no skin lesion is seen during the course of the disease. Children with PsA seem to display two different phenotypes. Younger children have a female predominance, ANA positivity and uveitis, while older children have more axial involvement.
Opposing Effects on Descending Control of Nociception by µ and κ Opioid Receptors in the Anterior Cingulate Cortex
Authors: Navratilova Edita , Qu Chaoling , Ji Guangchen , Neugebauer Volker , Guerrero Miguel , Rosen Hugh , Roberts Edward , Porreca Frank 
Published: September 2023

Background
The efficiency of descending pain modulation, commonly assessed with the conditioned pain modulation procedure, is diminished in patients with chronic pain. The authors hypothesized that the efficiency of pain modulation is controlled by cortical opioid circuits.

Methods
This study evaluated the effects of µ opioid receptor activation in the anterior cingulate cortex on descending control of nociception, a preclinical correlate of conditioned pain modulation, in male Sprague-Dawley rats with spinal nerve ligation–induced chronic pain or in sham-operated controls. Additionally, the study explored the consequences of respective activation or inhibition of κ opioid receptor in the anterior cingulate cortex of naive rats or animals with neuropathic pain. Descending control of nociception was measured as the hind paw withdrawal response to noxious pressure (test stimulus) in the absence or presence of capsaicin injection in the forepaw (conditioning stimulus).

Results
Descending control of nociception was diminished in the ipsilateral, but not contralateral, hind paw of rats with spinal nerve ligation. Bilateral administration of morphine in the anterior cingulate cortex had no effect in shams but restored diminished descending control of nociception without altering hypersensitivity in rats with neuropathic pain. Bilateral anterior cingulate cortex microinjection of κ opioid receptor antagonists, including nor-binaltorphimine and navacaprant, also re-established descending control of nociception in rats with neuropathic pain without altering hypersensitivity and with no effect in shams. Conversely, bilateral injection of a κ opioid receptor agonist, U69,593, in the anterior cingulate cortex of naive rats inhibited descending control of nociception without altering withdrawal thresholds.

Conclusions
Anterior cingulate cortex κ opioid receptor activation therefore diminishes descending control of nociception both in naive animals and as an adaptive response to chronic pain, likely by enhancing net descending facilitation. Descending control of nociception can be restored by activation of μ opioid receptors in the anterior cingulate cortex, but also by κ opioid receptor antagonists, providing a nonaddictive alternative to opioid analgesics. Navacaprant is now in advanced clinical trials.

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Diagnostic Accuracy of Smartphone Corneal Photography for Detection of Corneal Opacities in a Resource-Limited Setting: A Community-Based Study
Authors: Cao Binh , Giri Puspa , Byanju Raghunandan , Pradhan Sangita , Bhandari Gopal , Bhandari Sadhan , Kandel Ram Prasad , Poudyal Bimal , Gonzales John A. , Srinivasan Muthiah , Upadhyay Madan , Whitcher John P. , O'Brien Kieran S. , Lietman Thomas M. , Keenan Jeremy D. 
Published: September 2023

Purpose:
To evaluate the diagnostic accuracy of smartphone corneal photography in detecting corneal opacities in a community-based setting.

Methods:
A case-control, diagnostic accuracy study was nested in a cluster-randomized trial of a corneal ulcer prevention intervention in Nepal. Smartphone corneal photography was performed annually on community members self-reporting a potential risk factor for a corneal infection. Corneal photographs were graded for the presence or absence of an opacity. All cases with an opacity on smartphone photography and an equal number of controls were invited for a comprehensive eye examination with a slit lamp biomicroscope at an eye hospital. A mobile team visited participants unable to come to the hospital, conducting a limited examination with a penlight.

Results:
Of 1332 study participants (666 cases and 666 controls), 1097 had a penlight examination (535 cases and 562 controls) and 191 had a slit lamp examination (120 cases and 71 controls). When penlight examination was considered the reference standard, smartphone diagnosis of a corneal opacity had a positive predictive value (PPV) of 47% (95% confidence interval 43%–52%) and negative predictive value (NPV) of 95% (93%–97%). When slit lamp examination was considered the reference standard, the overall PPV and NPV were 71% (62%–78%) and 80% (70%–88%), respectively. The NPV was greater for detection of opacities >1 mm, estimated at 95% (90%–98%).

Conclusions:
Corneal photography performed in a resource-limited community-based setting using a smartphone coupled to an external attachment had acceptable diagnostic accuracy for detection of corneal opacities large enough to be clinically meaningful.
Bile acid–induced IRF3 phosphorylation mediates cell death, inflammatory responses, and fibrosis in cholestasis-induced liver and kidney injury via regulation of ZBP1
Authors: Zhuang Yuan , Ortega-Ribera Martí , Thevkar Nagesh Prashanth , Joshi Radhika , Huang Huihui , Wang Yanbo , Zivny Adam , Mehta Jeeval , Parikh Samir M. , Szabo Gyongyi 
Published: September 2023

Background and Aims:
Cell death and inflammation play critical roles in chronic tissue damage caused by cholestatic liver injury leading to fibrosis and cirrhosis. Liver cirrhosis is often associated with kidney damage, which is a severe complication with poor prognosis. Interferon regulatory factor 3 (IRF3) is known to regulate apoptosis and inflammation, but its role in cholestasis remains obscure. In this study.

Approach and Results:
We discovered increased IRF3 phosphorylation in the liver of patients with primary biliary cholangitis and primary sclerosing cholangitis. In the bile duct ligation model of obstructive cholestasis in mice, we found that tissue damage was associated with increased phosphorylated IRF3 (p-IRF3) in the liver and kidney. IRF3 knockout (Irf3

−/−
) mice showed significantly attenuated liver and kidney damage and fibrosis compared to wide-type mice after bile duct ligation. Cell-death pathways, including apoptosis, necroptosis, and pyroptosis, inflammasome activation, and inflammatory responses were significantly attenuated in Irf3
−/− mice. Mechanistically, we show that bile acids induced p-IRF3 in vitro in hepatocytes. In vivo, activated IRF3 positively correlated with increased expression of its target gene, Z-DNA–Binding Protein-1 (ZBP1), in the liver and kidney. Importantly, we also found increased ZBP1 in the liver of patients with primary biliary cholangitis and primary sclerosing cholangitis. We discovered that ZBP1 interacted with receptor interacting protein 1 (RIP1), RIP3, and NLRP3, thereby revealing its potential role in the regulation of cell-death and inflammation pathways. In conclusion.

Conclusions:
Our data indicate that bile acid–induced p-IRF3 and the IRF3-ZBP1 axis play a central role in the pathogenesis of cholestatic liver and kidney injury.
Research frontiers and hotspots in bacterial biofilm wound therapy: bibliometric and visual analysis for 2012–2022
Authors: Liu Rong , Zhai Linjun , Feng Shengya , Gao Rong , Zheng Jie 
Published: September 2023

Background:
Bacterial biofilms, which can protect bacteria from host immune response and drug attack, are an important factor in the difficult healing of chronic wound infection, which has become a major problem in medical development. This paper aimed to analyze literature related to bacterial biofilm wound treatment published between 2012 and 2022 using bibliometric and visual analysis.

Methods:
Publications related to bacterial biofilm wound treatment from 2012 to 2022 were selected from the Web of Science Core Collection. Microsoft Excel 2021, bibliometrics, CiteSpace6.1, and VOSviewer1.6.18 were used to extract and analyze data.

Results:
A total of 940 articles were published between 2012 and 2022, with the United States being the leading country (with 302 papers, 32.13%) and the University of Copenhagen in Denmark being the leading institution (with 26 published articles) in the field. Steven L Percival, a British academic, published the most articles (14). In the field of bacterial biofilm wound treatment, keywords suggested that the research gradually transitioned from lower limb venous ulcer, negative pressure-assisted healing to chronic wound, in-vitro bacterial biological model research, and then to the development of more microscopic and more advanced technologies such as antibacterial activity and nanomaterials. “Nanoparticles”, “inhibition/antibacterial”, “delivery”, “gold nanoparticles”, “hydrogel”, “wound healing”, etc., may become new research hotspots in this field.

Conclusion:
There is a lack of specific and effective treatment methods for diagnosing and treating bacterial biofilms in wounds. Through the development of multidisciplinary cooperation, early diagnosis and treatment of bacterial biofilms in wounds can be achieved. These data may provide a useful reference for scholars studying more effective bacterial biofilm wound treatment.
The clinical, genomic, and transcriptomic landscape of BRAF mutant cancers
Authors: Kazandjian Suzanne , Rousselle Emmanuelle , Dankner Matthew , Cescon David W. , Spreafico Anna , Ma Kim , Kavan Petr , Batist Gerald , Rose April A. N. 
Published: September 2023

AbstractBackgroundBRAF mutations are classified into 4 molecularly distinct groups, and Class 1 (V600) mutant tumors are treated with targeted therapies. Effective treatment has not been established for Class 2/3 or BRAF Fusions. We investigated whether BRAF mutation class differed according to clinical, genomic, and transcriptomic variables in cancer patients.MethodsUsing the AACR GENIE (v.12) cancer database, the distribution of BRAF mutation class in adult cancer patients was analyzed according to sex, age, primary race, and tumor type. Genomic alteration data and transcriptomic analysis was performed using The Cancer Genome Atlas.ResultsBRAF mutations were identified in 9515 (6.2%) samples among 153,834, with melanoma (31%), CRC (20.7%), and NSCLC (13.9%) being the most frequent cancer types. Class 1 harbored co-mutations outside of the MAPK pathway (TERT, RFN43) vs Class 2/3 mutations (RAS, NF1). Across all tumour types, Class 2/3 were enriched for alterations in genes involved in UV response and WNT/β-catenin. Pathway analysis revealed enrichment of WNT/β-catenin and Hedgehog signaling in non-V600 mutated CRC. Males had a higher proportion of Class 3 mutations vs. females (17.4% vs 12.3% q = 0.003). Non-V600 mutations were generally more common in older patients (aged 60+) vs younger (38% vs 15% p<0.0001), except in CRC (15% vs 30% q = 0.0001). Black race was associated with non-V600 BRAF alterations (OR: 1.58; p<0.0001).ConclusionsClass 2/3 BRAF are more present in Black, male patients with co-mutations outside of the MAPK pathway, likely requiring additional oncogenic input for tumorigenesis. Improving access to NGS and trial enrollment will help development of targeted therapies for non-V600 BRAF mutations.Statement of Translational RelevanceBRAF mutations are classified in 4 categories based on molecular characteristics, but only Class 1 BRAF V600 have effective targeted treatment strategies. With increasing access to next-generation sequencing, oncologists are more frequently uncovering non-V600 BRAF mutations, where there remains a scarcity of effective therapies. Responsiveness to MAPK pathway inhibitors differs according to BRAF mutation class and primary tumor type. For this reason, we sought to determine whether key demographic, genomic, and transcriptomic differences existed between classes. This cross-sectional study analyzes the largest dataset of BRAF-mutated cancers to date. Our findings propose insights to optimize clinical trial design and patient selection in the pursuit of developing effective treatment strategies for patients whose tumors harbor non-V600 BRAF mutations. This study also offers insights into the potential of targeting alternative pathways in addition to the MAPK pathway as part of combinatorial treatment strategies.
Specialty Organization Finances and Membership: A Closer Look
Authors: Syed Ali , Rahimy Ehsan , Sridhar Jayanth 
Published: September 2023

BackgroundUnited States students and physicians face massive financial hurdles including student loan repayments, board certification fees, and other expenses. This project investigates an infrequently discussed topic, the costs to join and the finances of national specialty organizations.PurposeWe hope our findings encourage resident physicians and newly minted attendings to take interest in the handling of the fees they may pay to join a national organization.MethodsPublicly available IRS 990 filings and specialty organization websites were examined to compile data regarding membership fees, organization revenue, expenses, and top earner salaries for 29 total specialty organizations. Descriptive and inferential statistics including Pearson correlation coefficients were used to investigate the above data.ResultsThe average annual revenue and net assets for the organizations studied were $50,762,279 and $66,444,291, respectively. The average annual membership fee was $542. The largest ratios of membership fee to physician salary were in pediatrics (0.31%) and ophthalmology (0.26%). The average salary of the top three earners at specialty organizations was $429,758.ConclusionsThere is wide variability in the costs of joining medical specialty organizations in the United States that does not correlate with the average earning potential of individual specialties. As a whole, medical specialty organizations should consider greater financial transparency.
AITeQ: A machine learning framework for Alzheimer’s prediction using a distinctive 5-gene signature
Authors: Ahammad Ishtiaque , Lamisa Anika Bushra , Bhattacharjee Arittra , Jamal Tabassum Binte , Arefin Md. Shamsul , Chowdhury Zeshan Mahmud , Hossain Mohammad Uzzal , Das Keshob Chandra , Keya Chaman Ara , Salimullah Md 
Published: September 2023

AbstractNeurodegenerative diseases, such as Alzheimer’s disease, pose a significant global health challenge with their complex etiology and elusive biomarkers. In this study, we developed the Alzheimer’s Identification Tool using RNA-Seq (AITeQ), a machine learning model based on an optimized random forest algorithm for identification of Alzheimer’s from RNA-Seq data. Analysis of RNA-Seq data from 433 individuals, including 293 Alzheimer’s patients and 140 controls led to the discovery of 47,929 differentially expressed genes. This was followed by a machine learning protocol involving feature selection, model training, performance evaluation, and hyperparameter tuning. The feature selection process undertaken in this study, employing a combination of 4 different methodologies, culminated in the identification of a compact yet impactful set of 5 genes. Ten diverse machine learning models were trained and tested using these 5 genes (ITGA10, CXCR4, ADCYAP1, SLC6A12, VGF). Performance metrics, including precision, recall, F1-score, accuracy, receiver operating characteristic area under the curve, and confusion matrices, were assessed before and after hyperparameter tuning. Overall, the random forest model with optimized hyperparameters was identified as the best and was used to develop AITeQ. AITeQ is available at:https://github.com/ishtiaque-ahammad/AITeQKey PointsA set of 5 genes (ITGA10, CXCR4, ADCYAP1, SLC6A12, VGF) were identified following differential gene expression and feature importance analysis.Ten diverse machine learning algorithms were trained and tested using the gene expression patterns of the identified 5 genes. The random forest algorithm with customized hyperparameters was found to be the best-performing model for differentiating Alzheimer’s disease samples from control.AITeQ, a user-friendly, reliable, and accurate machine learning framework for Alzheimer’s disease prediction was developed based on the 5 gene signature.
PSICHIC: physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data
Authors: Koh Huan Yee , Nguyen Anh T.N. , Pan Shirui , May Lauren T. , Webb Geoffrey I. 
Published: September 2023

ABSTRACTIn drug discovery, determining the binding affinity and functional effects of small-molecule ligands on proteins is critical. Current computational methods can predict these protein-ligand interaction properties but often lose accuracy without high-resolution protein structures and falter in predicting functional effects. We introduce PSICHIC (PhySIcoCHemICal graph neural network), a framework uniquely incorporating physicochemical constraints to decode interaction fingerprints directly from sequence data alone. This enables PSICHIC to attain first-of-its-kind emergent capabilities in deciphering mechanisms underlying protein-ligand interactions, achieving state-of-the-art accuracy and interpretability. Trained on identical protein-ligand pairs without structural data, PSICHIC matched and even surpassed leading structure-based methods in binding affinity prediction. In a library screening for adenosine A1 receptor agonists, PSICHIC discerned functional effects effectively, ranking the sole novel agonist within the top three. PSICHIC’s interpretable fingerprints identified protein residues and ligand atoms involved in interactions. We foresee PSICHIC reshaping virtual screening and deepening our understanding of protein-ligand interactions.
Validation of Dual Energy X-ray Absorptiometry for longitudinal quantification of tumor burden in a murine model of pancreatic ductal adenocarcinoma
Authors: Sechrist Zachary R. , Lee Grace , Schwarz Edward M. , Cole Calvin L. 
Published: September 2023

AbstractNoninvasive imaging is central to preclinical, in vivo models of pancreatic ductal adenocarcinoma (PDAC). While bioluminescent imaging (BLI) is a gold standard, its signal is dependent on the metabolic activity of tumor cells. In contrast, dual energy X-ray absorptiometry (DEXA) is a direct measure of body composition. Thus, we aimed to assess its potential for longitudinal quantification of tumor burden versus BLI. We utilized the KCKO murine model of PDAC and subjected tumor-bearing (n = 20) and non-tumor control (NTC) (n = 10) animals to weekly BLI and DEXA measurements for up to 10 weeks. While BLI detected tumors at 1-week, it failed to detect tumor growth, displayed a decreasing trend overtime (slope = -9.0x108; p = 0.0028), and terminal signal did not correlate with ex vivo tumor mass (r = 0.01853; p = 0.6286). In contrast, DEXA did not detect elevated changes in abdominal cavity lean mass until week 2 post inoculation and tumors were not visible until week 3, but successfully quantified a tumor growth trend (slope = 0.7322; p<0.0001), and strongly correlated with final tumor mass (r = 0.9351; p<0.0001). These findings support the use of BLI for initial tumor engraftment and persistence but demonstrate the superiority of DEXA for longitudinal tumor burden studies. As tumor detection by DEXA is not restricted to luciferase expressing models, future studies to assess its value in various cancer models and as an in vivo outcome measure of treatment efficacy are warranted.