bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable forage fish biomass and phenology influence marine predator diet, foraging behavior, and species interactions in coastal Newfoundland, Canada
Authors: Davoren Gail K 
Published: March 2024

Abstract
Forage fish species provide essential linkages for energy transfer within pelagic marine food webs. Capelin (Mallotus villosus), the focal forage fish in coastal Newfoundland, Canada, suffered a stock collapse in 1991 and has not recovered. Despite this collapse, capelin continue to provide locally abundant prey aggregations. Here, I synthesize the lessons learned from a long-term capelin-predator research program (2004–2022) on the northeast Newfoundland coast during the postcollapse period. I highlight the importance of simultaneously estimating forage fish biomass and predator responses in a multispecies and multiyear context. High interannual variation in capelin spawning timing and biomass was observed. Lower capelin biomass consistently resulted in predator species- and assemblage-level dietary shifts toward a higher diversity of lower trophic level, alternative prey. Energetic foraging costs of seabirds also increased under lower capelin biomass, but responses differed among species. Summer capelin consumption by dominant seabirds (9389 tonnes) and whales (778 tonnes) indicated predator energetic requirements and revealed higher natural mortality relative to fishery-based (1289 tonnes) mortality. Overall, this case study illustrated that, despite high observed behavioural plasticity, varying species-specific predator responses to changing capelin biomass integrated to increase potential competitive interactions under low capelin biomass, providing a basis for ecosystem-level change.
HIV Diagnostics and Vaccines: It Takes Two to Tango
Authors: Colón Will , Oriol-Mathieu Valérie , Hural John , Hattingh Lucy , Adungo Ferdinard , Lagatie Ole , Lavreys Ludo , Allen Mary , Anzala Omu , Espy Nicole , Fransen Katrien , Garcia Patricia J , Maciel Milton , Murtagh Maurine , Peel Sheila A , Peeling Rosanna W , Tan Litjen L J , Warren Mitchell , Pau Maria Grazia , D’Souza Patricia M 
Published: March 2024

Abstract
Current serologic tests for HIV screening and confirmation of infection present challenges to the adoption of HIV vaccines. The detection of vaccine-induced HIV-1 antibodies in the absence of HIV-1 infection, referred to as vaccine-induced seropositivity/seroreactivity, confounds the interpretation of test results, causing misclassification of HIV-1 status with potential affiliated stigmatization. For HIV vaccines to be widely adopted with high community confidence and uptake, tests are needed that are agnostic to the vaccination status of tested individuals (ie, positive only for true HIV-1 infection). Successful development and deployment of such tests will require HIV vaccine developers to work in concert with diagnostic developers. Such tests will need to match today's high-performance standards (accuracy, cost-effectiveness, simplicity) for use in vaccinated and unvaccinated populations, especially in low- and middle-income countries with high HIV burden. Herein, we discuss the challenges and strategies for developing modified serologic HIV tests for concurrent deployment with HIV vaccines.
Diversifying economic risks: Japan’s economic hedging toward China
Authors: Vidal López Lluc , Pelegrín Solé Àngels , Gonzalez-Pujol Ivan 
Published: March 2024

AbstractInternational Relations has traditionally identified balancing and bandwagoning as the two predominant strategies adopted by states in response to a rising power that threatens the status quo. However, recent academic debates have highlighted the emergence of hedging as a middle-ground approach adopted by states facing a rising power with ambiguous intentions, particularly when the stakes are high. Economic hedging forms a critical element of this strategy, as it allows states to maximize economic benefits while minimizing the risks of dependency through trade and investment. We present an analytical framework based on Kuik’s model, which focuses on the concept of economic diversification in trade and investment. We test its validity through an analysis of the diversification initiatives of the Abe administration and our central argument is that Japan’s diversification efforts are aimed at reducing economic risks and avoiding excessive dependency in specific sectors through trade and investment with China.
Sentence Completion as a User Experience Research Method: Recommendations From an Experimental Study
Authors: Schmidt Denise , Nebe Karsten , Lallemand Carine 
Published: March 2024

Abstract
The aim of this study is to investigate the use of the sentence completion technique (SCT) as a user experience (UX) research method. We conducted an online experiment (N = 400) to test the effect of sentence stem variations on sentence completion outcomes. Using a between-subjects design, half of the participants were exposed to impersonal sentence stems that did not include pronouns while the other half were exposed to stems formulated using first-person pronouns (PR). Additional hypotheses around stem formats (use of redundant stems, imaginative stems, two blanks stems, generic stems, stems prompting others’ perception) were tested using a within-subject design. The results do not support hypothesized differences between the pronoun and no pronoun condition. Findings however show that varying the format of the stem influences response behavior, as measured by variety, quantity and novelty of ideas, as well as the length of response. This study contributes to consolidating the use of SCT as a user research method and proposes actionable recommendations on how to create optimal sentence completion surveys in Human-Computer Interaction (HCI).
Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases
Authors: Perez-Enriquez Ricardo , Juárez Oscar E , Galindo-Torres Pavel , Vargas-Aguilar Ana Luisa , Llera-Herrera Raúl 
Published: March 2024

Abstract
The Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei is a highly relevant species for the world’s aquaculture development, for which an incomplete genome is available in public databases. In this work, PacBio long-reads from 14 publicly available genomic libraries (131.2 Gb) were mined to improve the reference genome assembly. The libraries were assembled, polished using Illumina short-reads, and scaffolded with P. vannamei, Feneropenaeus chinensis, and Penaeus monodon genomes. The reference-guided assembly, organized into 44 pseudo-chromosomes and 15,682 scaffolds, showed an improvement from previous reference genomes with a genome size of 2.055 Gb, N50 of 40.14 Mb, L50 of 21, and the longest scaffold of 65.79 Mb. Most orthologous genes (92.6%) of the Arthropoda_odb10 database were detected as “complete,” and BRAKER predicted 21,816 gene models; from these, we detected 1,814 single-copy orthologues conserved across the genomic references for Marsupenaeus japonicus, F. chinensis, and P. monodon. Transcriptomic-assembly data aligned in more than 99% to the new reference-guided assembly. The collinearity analysis of the assembled pseudo-chromosomes against the P. vannamei and P. monodon reference genomes showed high conservation in different sets of pseudo-chromosomes. In addition, more than 21,000 publicly available genetic marker sequences were mapped to single-site positions. This new assembly represents a step forward to previously reported P. vannamei assemblies. It will be helpful as a reference genome for future studies on the evolutionary history of the species, the genetic architecture of physiological and sex-determination traits, and the analysis of the changes in genetic diversity and composition of cultivated stocks.
Strangers’ property
Authors: Fabbri Marco , Dari-Mattiacci Giuseppe , Rizzolli Matteo 
Published: March 2024

AbstractWhy are impartial institutions such as formalized property rights so important for the emergence of impersonal trade? Previous literature has stressed the role of such institutions in providing third-party enforcement to shield strangers from locals’ opportunism. We document the existence of a second mechanism based on the role of formalized property rights in inducing respect for the property of strangers, regardless of enforcement. Ten years after the randomized introduction of formal property rights across rural Benin, we conducted a taking-dictator-game experiment in which participants could appropriate the endowment of an anonymous stranger from a different village. Even if enforcement institutions are absent and peer effects are silenced by design, participants from villages where the reform was implemented took significantly less than those in control villages. We further give consideration to several possible transmission channels and discuss their plausibility (JEL: D02, D91, K11, K42).
Increased platelet–CD8+ T-cell aggregates displaying high activation, exhaustion, and tendency to death correlate with disease progression in people with HIV-1
Authors: Wu Fengying , Li Yuanchun , Jiang Nan , Jiang Xu , Liu Xiaoqing , Dai Xiaopeng , Wang Fusheng 
Published: March 2024

Abstract
Platelets engage in HIV-1 infection by interacting with immune cells, which has been realized broadly. However, the potential interaction between platelets and CD8+ T cells remains unidentified. Here, treatment-naive individuals with HIV-1, complete immunological responders to antiretroviral therapy, and healthy controls were enrolled. First, we found that treatment-naive individuals with HIV-1 had low platelet numbers and high CD8+ T-cell counts when compared with complete immunological responders to antiretroviral therapy and healthy controls, leading to a low platelet/CD8+ T-cell ratio in peripheral blood, which could effectively differentiate the status of HIV-1 infection. Moreover, cytokines that may have been derived from platelets were higher in the plasma of people with HIV-1 despite viral suppression. Furthermore, we demonstrated that platelet–CD8+ T-cell aggregates were elevated in treatment-naive individuals with HIV-1, which positively correlated with HIV-1 viral load but negatively correlated with CD4+ T-cell count and CD4/CD8 ratio. Finally, we revealed that platelet–CD8+ T-cell aggregates correlate with enhanced activation/exhaustion and pyroptosis/apoptosis compared with free CD8+ T cells. Moreover, platelet-induced caspase 1 activation of CD8+ T cells correlated with IL-1β and IL-18 plasma levels. In brief, we reveal the importance of platelets in HIV-1 infection, which might secrete more cytokines and mediate CD8+ T-cell phenotypic characteristics by forming platelet–CD8+ T-cell aggregates, which are related to poor prognosis.
Effective alignment method using a diamond notch knife for correlative array tomography
Authors: Goto Yumi , Takeda-Kamiya Noriko , Yamaguchi Kaori , Yamazaki Mikio , Toyooka Kiminori 
Published: March 2024

Abstract
Correlative array tomography, combining light and electron microscopy via serial sections, plays a crucial role in the three-dimensional ultrastructural visualization and molecular distribution analysis in biological structures. To address the challenges of aligning fluorescence and electron microscopy images and aligning serial sections of irregularly shaped biological specimens, we developed a diamond notch knife, a new tool for puncturing holes using a diamond needle. The diamond needle featured a triangular and right-angled tip, enabling the drilling of deep holes upon insertion into the polished block face. This study describes the application of the diamond notch knife in correlative array tomography.
All hands on deck: the role of collaborative platforms and lead organizations in achieving environmental goals
Authors: Lee Heewon , Liu Yixin 
Published: March 2024

Abstract
This study examines the effectiveness of collaborative platforms in supporting local collaborations for natural resource management. It also explores how governmental and non-governmental lead organizations adopt differing collaborative implementation approaches and how these variations influence outcomes. Utilizing a natural experiment and a difference-in-differences estimator, we evaluate if the Department of Energy’s Clean Cities program functions as a collaborative platform to foster local-level Clean Cities Collaborations across the US, thereby improving air quality. Our findings suggest that Clean Cities Collaborations have a substantial and enduring impact on reducing air pollution. A series of subgroup analyses suggests that these environmental improvements are most noticeable in collaborations led by non-profits and regional government councils, rather than those directed by state and local governments. A complementary content analysis provides exploratory evidence that issue definition, collaborative group structure, and inclusive decision-making processes are crucial managerial factors that contribute to the environmental improvements. These insights pave the way for more effective management of collaborative governance on a larger scale.
Incidental finding of an ectopic b2 thymoma attached to the pericardium
Authors: Endara Santiago A , Davalos Gerardo A , Ponton M Patricia , Gordon Christian I , Molina Gabriel A 
Published: March 2024

Abstract
Ectopic thymoma is a rare tumor that arises from the abnormal migration of thymus tissue. They are extremely rare and have a broad spectrum of clinical symptoms. Therefore, preoperative diagnosis is complex and can be easily misdiagnosed. Complete resection is the treatment of choice to avoid recurrence, radiotherapy and enhanced survival. Regretfully, many patients arrive at a late stage, limiting our therapeutic options; therefore, pre-operative diagnosis is vital. We present the case of an otherwise healthy 32-year-old woman; after a chest X-ray was done for a routine medical evaluation, a mass was discovered in her mediastinum. After surgery, a B2 thymoma attached to the pericardium was discovered and successfully treated.
Eosinophilic gastritis in adult complicated by gastric ulcer perforation
Authors: Tharakan Joseph A , O’Toole Julianna P , Kharoud Harmeet K , Bunker Mark L , Chen Jennifer Y , Yokota Shinichiro 
Published: March 2024

Abstract
Eosinophilic gastritis is a rare type of eosinophilic gastrointestinal diseases. Patients with eosinophilic gastritis usually present with symptoms such as nausea, emesis, abdominal pain, and weight loss. In severe cases, patients can suffer rare complications such as gastric outlet obstruction and spontaneous perforation. Here, we present the case of a young adult male who presented with acute onset abdominal pain for 1 day. The patient was found to have significant mural thickening of gastric antrum with pneumoperitoneum on abdominal CT scan, consistent with a perforated gastric ulcer. The patient underwent exploratory laparotomy and required modified graham patch repair. The diagnosis of eosinophilic gastritis was made based on the pathology review of intraoperative endoscopic biopsy specimens.
BMP4 and GREM1 are targets of SHH signaling and downstream regulators of collagen in the penis
Authors: Deng Jiangping , Searl Timothy , Ohlander Samuel , Dynda Danuta , Harrington Daniel A , McVary Kevin T , Podlasek Carol A 
Published: March 2024

Abstract

Background
Cavernous nerve (CN) injury, caused by prostatectomy and diabetes, initiates a remodeling process (smooth muscle apoptosis and increased collagen) in the corpora cavernosa of the penis of patients and animal models that is an underlying cause of erectile dysfunction (ED), and the Sonic hedgehog (SHH) pathway plays an essential role in the response of the penis to denervation, as collagen increases with SHH inhibition and decreases with SHH treatment.

Aim
We examined if part of the mechanism of how SHH prevents penile remodeling and increased collagen with CN injury involves bone morphogenetic protein 4 (BMP4) and gremlin1 (GREM1) and examined the relationship between SHH, BMP4, GREM1, and collagen in penis of ED patients and rat models of CN injury, SHH inhibition, and SHH, BMP4, and GREM1 treatment.

Methods
Corpora cavernosa of Peyronie’s disease (control), prostatectomy, and diabetic ED patients were obtained (N = 30). Adult Sprague Dawley rats (n = 90) underwent (1) CN crush (1-7 days) or sham surgery; (2) CN injury and BMP4, GREM1, or mouse serum albumin (control) treatment via Affi-Gel beads or peptide amphiphile (PA) for 14 days; (3) 5E1 SHH inhibitor, IgG, or phosphate-buffered saline (control) treatment for 2 to 4 days; or (4) CN crush with mouse serum albumin or SHH for 9 days.

Outcomes
Immunohistochemical and Western analysis for BMP4 and GREM1, and collagen analysis by hydroxyproline and trichrome stain were performed.

Results
BMP4 and GREM1 proteins were identified in corpora cavernosa smooth muscle of prostatectomy, diabetic, and Peyronie’s patients, and in rat smooth muscle, sympathetic nerve fibers, perineurium, blood vessels, and urethra. Collagen decreased 25.4% in rats with CN injury and BMP4 treatment (P = .02) and increased 61.3% with CN injury and GREM1 treatment (P = .005). Trichrome stain showed increased collagen in rats treated with GREM1. Western analysis identified increased BMP4 and GREM1 in corpora cavernosa of prostatectomy and diabetic patients, and after CN injury (1-2 days) in our rat model. Localization of BMP4 and GREM1 changed with SHH inhibition. SHH treatment increased the monomer form of BMP4 and GREM1, altering their range of signaling.

Clinical implications
A better understanding of penile remodeling and how fibrosis occurs with loss of innervation is essential for development of novel ED therapies.

Strengths and limitations
The relationship between SHH, BMP4, GREM1, and collagen is complex in the penis.

Conclusion
BMP4 and GREM1 are downstream targets of SHH that impact collagen and may be useful in collaboration with SHH to prevent penile remodeling and ED.
SHH regulates penile morphology and smooth muscle through a mechanism involving BMP4 and GREM1
Authors: Deng Jiangping , Martin Sarah , Searl Timothy , Ohlander Samuel , Harrington Daniel A , McVary Kevin T , Podlasek Carol A 
Published: March 2024

Abstract

Background
The cavernous nerve (CN) is frequently damaged in prostatectomy and diabetic patients with erectile dysfunction (ED), initiating changes in penile morphology including an acute and intense phase of apoptosis in penile smooth muscle and increased collagen, which alter penile architecture and make corpora cavernosa smooth muscle less able to relax in response to neurotransmitters, resulting in ED.

Aim
Sonic hedgehog (SHH) is a critical regulator of penile smooth muscle, and SHH treatment suppresses penile remodeling after CN injury through an unknown mechanism; we examine if part of the mechanism of how SHH preserves smooth muscle after CN injury involves bone morphogenetic protein 4 (BMP4) and gremlin1 (GREM1).

Methods
Primary cultures of smooth muscle cells were established from prostatectomy, diabetic, hypertension and Peyronie’s (control) (N = 18) patients. Cultures were characterized by ACTA2, CD31, P4HB, and nNOS immunohistochemical analysis. Patient smooth muscle cell growth was quantified in response to BMP4 and GREM1 treatment. Adult Sprague Dawley rats underwent 1 of 3 surgeries: (1) uninjured or CN-injured rats were treated with BMP4, GREM1, or mouse serum albumin (control) proteins via Affi-Gel beads (N = 16) or peptide amphiphile (PA) (N = 26) for 3 and 14 days, and trichrome stain was performed; (2) rats underwent sham (N = 3), CN injury (N = 9), or CN injury and SHH PA treatment for 1, 2, and 4 days (N = 9).

Outcomes
Western analysis for BMP4 and GREM1 was performed; (3) rats were treated with 5E1 SHH inhibitor (N = 6) or IgG (control; N = 6) for 2 and 4 days, and BMP4 and GREM1 localization was examined. Statistics were performed by analysis of variance with Scheffé’s post hoc test.

Results
BMP4 increased patient smooth muscle cell growth, and GREM1 decreased growth. In rats, BMP4 treatment via Affi-Gel beads and PA increased smooth muscle at 3 and 14 days of treatment. GREM1 treatment caused increased collagen and smooth muscle at 3 days, which switched to primarily collagen at 14 days. CN injury increased BMP4 and GREM1, while SHH PA altered Western band size, suggesting alternative cleavage and range of BMP4 and GREM1 signaling. SHH inhibition in rats increased BMP4 and GREM1 in fibroblasts.

Clinical implications
Understanding how SHH PA preserves and regenerates penile morphology after CN injury will aid development of ED therapies.

Strengths and limitations
SHH treatment alters BMP4 and GREM1 localization and range of signaling, which can affect penile morphology.

Conclusion
Part of the mechanism of how SHH regulates corpora cavernosa smooth muscle involves BMP4 and GREM1.
HIV/AIDS
Authors: Fidler Sarah , Peto Timothy E.A. , Goulder Philip , Conlon Christopher P. 
Published: March 2024

Abstract
Since its discovery in 1983, the human immunodeficiency virus (HIV) has been associated with a global pandemic that has affected more than 80 million people and caused more than 37 million deaths. Globally, 37.7 million (30.2–45.1 million) people were living with HIV at the end of 2020. New HIV infections globally have reduced by 52% since the peak in 1997. In 2020, around 1.5 million people were newly infected with HIV. An estimated 0.8% of adults aged 15–49 years worldwide are living with HIV, although the burden of the epidemic continues to vary considerably between countries and regions. Sub-Saharan Africa remains most severely affected, with nearly 1 in every 20 adults living with HIV and accounting for nearly 71% of the people living with HIV worldwide. The impact of HIV in some African countries has been sufficient to reverse population growth and reduce life expectancy into the mid-30s, although HIV incidence has declined in some of these high-prevalence countries. However, there are large-scale HIV epidemics elsewhere (e.g. India, the Russian Federation, and Eastern Europe). AIDS-related deaths have been reduced by 64% from the peak in 2004 through global access to antiretroviral therapy (ART). Global access to ART has improved dramatically; in 2020, 84% of people living with HIV knew their status, and amongst those people who knew their status, 87% were accessing ART, with 66% on successful therapy with a suppressed HIV viral load.
Cystic fibrosis
Authors: Bush Andrew , Elston Caroline 
Published: March 2024

Abstract
Cystic fibrosis (CF) is a recessively inherited disease caused by mutations in the cystic fibrosis gene, located on the long arm of chromosome 7, which codes for a membrane protein—the cystic fibrosis transmembrane regulator protein—that is a chloride channel. More than 2,000 CF mutations have been identified, with the F508del mutation being the most common of around approximately 300 mutations that definitely cause disease (70% of CF chromosomes in the European population). Birth incidence varies with country of origin from 1 in 2,000 to 1 in 100,000. The most popular hypothesis is that mutant cystic fibrosis transmembrane regulator protein fails to transport chloride ions normally, and there is secondary impairment of sodium, bicarbonate, and water transport. Prognosis is being transformed by early diagnosis on newborn screening and novel gene subclass-specific molecular therapies.