bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fannyhessea vaginae and clearance of Lactobacillus iners are associated with incident non-chlamydial non-Mycoplasma genitalium urethritis in men who have sex with women
Authors: Drover Caitlin M. , Srinivasan Sujatha , Tapia Kenneth A. , Munch Matthew , Rowlinson Emily , Chambers Laura C. , Fiedler Tina L. , Lowens M. Sylvan , Khosropour Christine M. , Manhart Lisa E , Fredricks David N. 
Published: December 2024

Abstract

Background
The etiology of nongonococcal urethritis (NGU) is incompletely understood. We sought to determine if genitourinary bacterial diversity or specific taxa were associated with incident NGU.

Methods
From August 2014-July 2018, men who have sex with women attending a sexual health clinic were clinically evaluated, including Mycoplasma genitalium (MG) and Chlamydia trachomatis (CT) testing, at enrollment and six monthly visits. New cases of NGU (≥5 PMNs/HPF in urethral exudates plus either symptoms or visible discharge) and their visit preceding NGU diagnosis were matched 1:1 to two sequential visits without NGU (controls). We determined associations with incident NGU and applied broad-range 16S rRNA gene polymerase chain reaction and sequencing to urine samples from each visit. We used conditional logistic regression to evaluate the association of Shannon Diversity Index (SDI), species richness, Haemophilus influenzae, Fannyhessea vaginae, Lactobacillus iners, and Streptococcus mitis group with incident non-CT-non-MG-NGU (NCNM-NGU).

Results
Of 62 matched case-control pairs, median age was 32. Higher SDI the previous month was associated with higher odds of incident NCNM-NGU (adjusted odds ratio [aOR] = 2.8 per unit increase; 95% CI = 1.03-7.47), as was F. vaginae at NGU diagnosis (aOR = 5.1; 95% CI = 1.28-20.15), F. vaginae acquisition (aOR = 13.8; 95% CI = 1.96-97.33) and consistent carriage of F. vaginae (aOR = 16.1; 95% CI = 1.66-156.29). Odds of NCNM-NGU were higher when L. iners cleared between visits (aOR = 18.0; 95% CI = 1.08-299.24). Neither H. influenzae nor S. mitis group were associated with incident NCNM-NGU.

Conclusions

F. vaginae acquisition/detection and L. iners clearance were associated with urethritis. This merits investigation in larger longitudinal studies using species-specific detection methods.
An evaluation of syphilis partner services among gay, bisexual, and other men who have sex with men with early syphilis in King County, WA
Authors: Kerani Roxanne P. , Chang Alene , Berzkalns Anna , Moreno Juan Palacios , Ramchandani Meena , Golden Matthew R. 
Published: December 2024

Abstract

Background
Partner services (PS) have been integral to syphilis control in the U.S. since the early 20th century but have not been evaluated in a controlled study.

Methods
We compared PS outcomes among gay, bisexual, and other men who have sex with men (GBMSM) diagnosed with syphilis from May 2020-June 2021 for whom health department staff initiated PS efforts (PS group) and a randomly selected control group for whom no PS efforts were initiated. We interviewed participants about partner outcomes and used chi-square tests and Poisson regression to test for differences in outcomes between groups.

Results
We attempted to contact 350 GBMSM and offered participation to 184 men, of whom 92 (51%) participated, including 41 men in the PS group and 51 controls. The percentage of participants who reported notifying >1 sex partner after diagnosis was similar in the PS and control groups (83% vs. 80%, p = 0.80). Mean number of partners notified or tested did not differ between PS and control groups (notified mean[range]: 2.5 [0-10] vs 3.3 [0-20], p = 0.16; tested mean[range]: 1.2 [0-8] vs. 1 [0-10], p = 0.66); multivariate results were similar. Among those contacted for PS, approximately half (48%) reported PS staff helped them with medical care for syphilis, and 31% said that PS staff connected them to PrEP.

Conclusions
This small, controlled evaluation suggests that syphilis PS may have no impact on partner treatment among GBMSM, though most men support the intervention. A randomized trial is needed to definitively define the contemporary effectiveness of syphilis PS among GBMSM.
Cold Storage Disrupts the Proteome and Phosphoproteome Landscape in Rat Kidney Transplants
Authors: Sharma Amod , Jun Se-Ran , Bhattarai Dinesh , Panday Sudip , Venugopal Gopinath , Panawan Orasa , Washam Charity , Mackintosh Samuel , Byrum Stephanie , Udaondo Zulema , Arthur John M. , MacMillan-Crow Lee Ann , Parajuli Nirmala 
Published: December 2024

Background.
Prolonged cold storage (CS) of kidneys results in poor long-term outcomes after transplantation (Tx). We reported previously that CS of rat kidneys for 18 h before transplant impaired proteasome function, disrupted protein homeostasis, and reduced graft function. The goal of the present study was to identify the renal proteins, including phosphoproteins, that are dysregulated by this CS injury.

Methods.
Isolated donor Lewis rat kidneys were subject to 18 h CS and transplanted into recipient Lewis rats (CS + Tx). Autotransplantation (transplant with 0 h CS) or Sham (right nephrectomy) surgeries served as controls. The proteome of kidney homogenates was analyzed with tandem mass-tag mass spectrometry to identify CS-induced abnormalities in kidney grafts.

Results.
CS injury disrupted the renal proteome/phosphoproteome landscape in kidney grafts and dysregulated numerous signaling pathways. We identified 3217 phosphopeptides (with 1398 novel phosphosites) that were significantly dysregulated in a CS-specific manner. In particular, proteins and pathways such as complement system and mitogen-activated protein kinases, including p38MAPK, were upregulated, whereas antioxidant/metabolic pathways, such as glutathione, were suppressed in CS + Tx groups compared with autotransplantation and sham controls.

Conclusions.
This study provides deeper insight into the disruption of the renal proteome/phosphoproteome caused by CS injury and provides a novel set of pathways and molecules, including p38MAPK, that can be investigated to delineate their specific role in renal transplant outcomes, ultimately improving outcomes for patients with end-stage kidney disease.
Visual Functions in Patients With Leber Hereditary Optic Neuropathy (LHON)
Authors: Francomme Robin , Lenoble Quentin , Smirnov Vasily , Boucart Muriel 
Published: December 2024

Background:
Most of the data on visual functions in Leber hereditary optic neuropathy (LHON) is based on patient questionnaires. Our study assessed the impact of LHON on visual function by testing facial recognition and execution of purposeful actions.

Methods:
Twelve participants with LHON with central scotoma ranging from 5° to 20° and 12 unaffected age-matched controls were involved in our study. In the face recognition test, participants were asked to recognize the sex and the facial expression of photographs of faces increasing in size to simulate approaching faces. In the purposeful action test, they were asked to manipulate real objects while their eye movements were recorded.

Results:
Although most patients were able to recognize the correct sex of a face at a size corresponding to a 1-m viewing distance, recognition of facial expressions was severely impaired. Patients were slower than control subjects in executing purposeful tasks. A dynamic strategy to sample information needed for the execution of a task was documented in a longer scanpath and in higher frequency of saccades and fixation eye movements in patients than in control subjects.

Conclusions:
Face perception is strongly impaired in patients with LHON. In addition, although the selection and manipulation of real objects to execute a task are slowed, they can be performed efficiently using peripheral vision.
A Comparative Analysis of Privacy-Preserving Large Language Models For Automated Echocardiography Report Analysis
Authors: Mahmoudi Elham , Vahdati Sanaz , Chao Chieh-Ju , Khosravi Bardia , Misra Ajay , Lopez-Jimenez Francisco , Erickson Bradley J. 
Published: December 2024

AbstractBackgroundAutomated data extraction from echocardiography reports could facilitate large-scale registry creation and clinical surveillance of valvular heart diseases (VHD). We evaluated the performance of open-source Large Language Models (LLMs) guided by prompt instructions and chain of thought (CoT) for this task.MethodsFrom consecutive transthoracic echocardiographies performed in our center, we utilized 200 random reports from 2019 for prompt optimization and 1000 from 2023 for evaluation. Five instruction-tuned LLMs (Qwen2.0-72B, Llama3.0-70B, Mixtral8-46.7B, Llama3.0-8B, and Phi3.0-3.8B) were guided by prompt instructions with and without CoT to classify prosthetic valve presence and VHD severity. Performance was evaluated using classification metrics against expert-labeled ground truth. Mean Squared Error (MSE) was also calculated for predicted severity’s deviation from actual severity.ResultsWith CoT prompting, Llama3.0-70B and Qwen2.0 achieved the highest performance (accuracy: 99.1% and 98.9% for VHD severity; 100% and 99.9% for prosthetic valve; MSE: 0.02 and 0.05, respectively). Smaller models showed lower accuracy for VHD severity (54.1-85.9%) but maintained high accuracy for prosthetic valve detection (>96%). CoT reasoning yielded higher accuracy for larger models while increasing processing time from 2-25 to 67-154 seconds per report. Based of CoT reasonings, the wrong predictions were mainly due to model outputs being influenced by irrelevant information in the text or failure to follow the prompt instructions.ConclusionsOur study demonstrates the near-perfect performance of open-source LLMs for automated echocardiography report interpretation with purpose of registry formation and disease surveillance. While larger models achieved exceptional accuracy through prompt optimization, practical implementation requires balancing performance with computational efficiency.
Clinical Characteristics ofEYS-Associated Retinal Dystrophy in 295 Japanese Patients
Authors: Koyanagi Yoshito , Murakami Yusuke , Kominami Taro , Fukushima Masatoshi , Goto Kensuke , Yokota Satoshi , Mizobuchi Kei , Mawatari Go , Torii Kaoruko , Inoue Yuji , Ota Junya , Okuda Daishi , Fujiwara Kohta , Yamaga Hanayo , Hisai Takahiro , Endo Mikiko , Iijima Hanae , Kaida Tomoko , Miyata Kazunori , Nakazaki Shuji , Hayashi Takaaki , Hirami Yasuhiko , Akiyama Masato , Terao Chikashi , Momozawa Yukihide , Sonoda Koh-Hei , Nishiguchi Koji M , Ikeda Yasuhiro 
Published: December 2024

AbstractObjectiveTo describe the clinical characteristics of Inherited retinal dystrophy (IRD) caused byEYS(EYS–RD), the most common causative gene of this disease in the Japanese population.DesignA multicenter retrospective studyParticipants295 patients (143 men and 152 women) withEYS–RD registered in the Japan Retinitis Pigmentosa Registry Project at eight Japanese facilities.MethodsWe evaluated age at the first visit, duration of observation, age of onset, first symptoms, family history, history of consanguineous marriage, disease type, macular complications, history of cataract surgery, logarithm of the minimum angle of resolution best-corrected visual acuity (logMAR BCVA), and its progression. The mean ± standard deviation or the proportion of each parameter was calculated and compared across different variant levels.Main Outcome MeasuresClinical parameters including age of onset, BCVA, and progression of BCVA.ResultsThe mean age at the first visit was 45.5 ± 14.9 years, and the mean duration of observation was 7.7 ± 6.2 years. The mean age at disease onset was 25.5 ± 14.7 years. The first symptoms ofEYS–RD included night blindness (78.5%), visual field impairment (9.6%), and loss of visual acuity (8.0%). Family history and consanguineous marriages accounted for 29.7% and 9.3% of the patients, respectively. Rod-cone dystrophy and cone-rod dystrophy accounted for 96.3% and 2.4% of patients, respectively. The mean logMAR BCVA was 0.33 ± 0.56, and the mean progression was 0.03 ± 0.07 per year. In variant-based analyses, three East Asian–specific pathogenic variants (S1653fs, Y2935X, and G843E) caused 69.7% of JapaneseEYS–RD patients. In cases with homozygous pathogenic variants, the mean age at onset was 17.9, 27.5, and 26.2 years, and the mean progression of logMAR BCVA was 0.05 ± 0.09, 0.04 ± 0.06, and 0.04 ± 0.05 per year for S1653fs (n = 31), Y2935X (n = 13), and G843E (n = 24), respectively.ConclusionsWe described the clinical characteristics of Japanese patients withEYS–RD. The clinical differences among major East Asian–specific pathogenic variants indicate the utility of genetic testing in personalized medicine for IRD patients tailored to population characteristics.
Trapline foraging by nectar-collecting hornets
Authors: Lacombrade Mathilde , Abenis Kristine , Doussot Charlotte , Goulefert Loïc , Nanba Kenji , Bonzom Jean-Marc , Lihoreau Mathieu 
Published: December 2024

AbstractCentral place foraging bees, butterflies, birds and bats are known to develop routes in order to visit familiar plant resources in a stable and repeatable order called “traplines”. Here we report a similar behaviour in a social wasp, the Japanese yellow hornetVespa simillima. We monitored the foraging movements of individually marked wild hornets collecting sucrose solution on four artificial flowers placed in the field. After thirty foraging bouts, all the hornets had developed a repeatable flower visitation sequence. Using two different arrays of flowers, we show how hornets increase their foraging efficiency through time but do not always use the shortest path to visit all flowers, often favoring movements between nearest neighbor flowers over global path optimization. Our study adds nectar-foraging wasps to the growing list of animals developing traplines thereby opening new perspectives for comparative cognition research.
Mechanism of SHP2 activation by bis-Tyr-phosphorylated Gab1
Authors: Machner Lisa , Shaikhqasem Alaa , Gruber Tobias , Hamdi Farzad , Breithaupt Constanze , Kniest Judith , Wiebe Felix , Lewitzky Marc , Parthier Christoph , Kyrilis Fotis L. , Balbach Jochen , Kastritis Panagiotis L. , Feller Stephan M. , Stubbs Milton T. 
Published: December 2024

AbstractThe non-receptor tyrosine phosphatase SHP2 (PTPN11) is a regulator of diverse cellular functions including mitogenic activation and cell migration. SHP2 consists of two tandem SH2 domains followed by the catalytic domain, and is autoinhibited by the N-terminal SH2 domain that blocks access to the active site. Mutations that influence auto-inhibition have been implicated in cancer and other diseases, and allosteric inhibitors have been developed that stabilise the inactive state. The mechanism of SHP2 activation remains unclear, however. Here, we show that the intrinsically disordered bis-phosphorylated SHP2-activating peptide pY627pY659-Gab1 binds to both SH2 domains, undergoing a partial disorder-to-order transition in the process. In addition to eliciting changes in SH2 domain dynamics, the peptide reorganises their relative orientations to provide a new SH2-SH2 interface. Our data suggest an active conformation for SHP2 that is also applicable to the hematopoietic cell-specific SHP1 (PTPN6), shedding light on the activation mechanism of both enzymes and paving the way for the development of novel compounds that modulate SHP2 activity.
Lipid bilayers determine the allostery but not intrinsic affinity of cAMP binding to pacemaker channels
Authors: Idikuda Vinay , Roy Chowdhury Susovan , Chang Yongchang , Ren Qian , Bao Huan , Goldsmith Randall H. , Chanda Baron 
Published: December 2024

AbstractIn the human heart, the binding of cyclic adenosine monophosphate (cAMP), a second messenger, to hyperpolarization and cyclic nucleotide-gated (HCN) regulates the automaticity of pacemaker cells. Recent single-molecule binding studies show that cAMP bound to each subunit of purified tetrameric HCN channels independently, in contrast to findings in cells. To explore the lipid membrane’s role in cAMP regulation, we reconstituted purified human HCN channels in various lipid nanodiscs and resolved single molecule ligand-binding dynamics. Our measurements show that lipid membranes promote cooperative binding of cAMP to HCN channels without altering the intrinsic binding affinity. Cryo-EM structures of HCN channels in lipid nanodiscs reveal enhanced inter-subunit interactions, underscoring the fundamental role of lipid membranes in amplifying the gating sensitivity of ion channels.
Deciphering the molecular mechanism associated with the interaction of TULP3 and Histone deacetylases, SIRT1 and SIRT2
Authors: Manjula Ramu , Krishnappa Gopinatha , Sriram Vikeraman , Balasundaram Padmanabhan 
Published: December 2024

AbstractTubby-like protein-3 (TULP3), a member of the tubby family, is recognized for its role in ciliary trafficking, linking membrane-associated proteins to the intraflagellar transport complex A (IFT-A). Mammalian tubby family proteins (TULP1-4), featuring a C-terminal tubby domain, play crucial roles in intracellular transport, signaling, cell differentiation, and motility. TULP3 is also associated with renal and hepatic fibrocystic disease and liver, kidney, and heart degeneration. However, the modulation of TULP3 function and its interacting partners in the cell still need to be understood. Recent studies have indicated interactions between TULP3 and various proteins, including acetylating and deacetylating enzymes. In this study, we investigate the interaction of TULP3 with Sirtuins, SIRT1, and SIRT2 using biochemical and biophysical techniques. Our findings revealed that both the N- and C-terminal domains of TULP3 are necessary for the interaction with SIRT1 and SIRT2. Furthermore, we have identified that TULP3 is not a deacetylation substrate for SIRT1.
Distinct ecotoxicological impairs induced by differentMicrocystisgenotypes to Medaka fish
Authors: Marie Benjamin , Meur Maiwenn Le , Duval Charlotte , Quiquand Manon , Lance Emilie , Duperron Sébastien 
Published: December 2024

AbstractOne of the most prevalent and notorious bloom-forming freshwater cyanobacterial genus isMicrocystis, whom toxicological impairs yet remain incompletely investigated. Based on our previous studies, we hypothesize that some emergingMicrocystismetabolites, in addition to microcystins (MCs), are of (eco)toxicological concerns and should be further investigated. To this end, we explore the ecotoxicological potential of differentMicrocystisgenotypes producing various bio-active metabolite cocktails, particularly cyanopeptides of different structural families including MCs, cyanopeptolins, microginins, anabaenopetins, aeruginosins or microcyclamides, on embryo/larvae and adult Medaka fish model.Embryo and larvae exposures to the extracts of the four distinctMicrocystisgenotypes - comprising two MC-producing (PMC 728.11 and 807.12) and two non-MC-producing (PMC 810.12 and 826.12) strains – showed that PMC 810.12 and 826.12 respectively producing microginins, aeruginosins and microcyclamides exhibit early toxicity and teratogenicity, while PMC 728.11 presented rather larvae toxicity on hatched larvae, in agreement with its high MC content. In addition, we conducted a 4-days microcosm experiment with adult female Medaka exposed to environmental concentrations of these fourMicrocystisstrain cultures to document the microbiome and metabolome responses. Fishes exposed to PMC 728.11 exhibited microbiota dysbiosis signature, while exposure to PMC 826.12 perturbated the fish digestion process inducing even more pronounced microbial and metabolic alterations. The two other strains provoked more moderate perturbations. These findings highlight toxic effects on fish exposed to both MC-as well as non-MC-producing cyanobacteria, suggesting complex interplay and effects of undocumented cyanobacterial bio-active and toxic compounds basides MCs during blooms ofMicrocystis.
The change of consumer-domestic brand attitude under the influence of multi-period public opinion events: evidence from Chinese fast-fashion clothing brands
Authors: Han Zhao 
Published: December 2024

PurposeThis study aims to conduct a dynamic analysis of consumer attitudes towards domestic brands under the influence of multiple-period opinion events, providing methodological guidance for the overall development of fast-fashion clothing brands.Design/methodology/approachThis study takes the Xinjiang cotton event and ERKE donation event in 2021 as the samples and Weibo comments on the hot topic of the fact that ANTA’s total turnover exceeded NIKE’s on the 2021 Double 11 as the first and explores the process and influencing factors of consumer domestic brand attitude change through latent Dirichlet allocation (LDA) model.FindingsUnder the influence of multiple public opinion events, consumers’ attitudes towards domestic brands experienced changes from brand awareness and brand identification to brand loyalty. First of all, patriotism and the awareness of Chinese goods lead to consumers’ brand awareness. The social responsibility and perceived quality of the later stage will stimulate consumers’ brand identification. Finally, the matching of national pride and perceived products will promote consumers’ brand loyalty.Originality/valueThis study establishes a model of the evolution of consumer attitudes towards domestic brands, revealing for the first time from a dynamic perspective the factors influencing these attitudes. This study offers a novel perspective on the processes and structures of the relationship between consumers and domestic brands.
Transitioning to a circular economy in the construction demolition industry: a bibliometric analysis
Authors: Sadiq Muhammad , Khalfan Malik Mansoor Ali 
Published: December 2024

PurposeThis study aims to address the research gaps in the application of circular economy (CE) principles within the construction demolition industry (CDI) by providing an updated overview of key themes, trends and challenges. Using a bibliometric approach, it seeks to highlight the transformative potential of CE adoption in CDI, focusing on strategies for waste reduction, resource efficiency and supply chain optimization to support sustainable development.Design/methodology/approachBibliometric analysis using the Scopus database was employed to systematically review the literature on CE principles in the CDI from 2014 to 2023. The analysis involved a four-step assessment, including qualitative reviews and quantitative evaluations, to identify key themes, trends, challenges and opportunities in CE research within the CDI. The intricate relationship between CE principles with a specific emphasis on CDI, building practices and supply chain management was explored.FindingsThe findings underscore a significant emphasis on circularity principles, interdisciplinary collaboration and the integration of emerging technologies for efficient waste management. Experiencing a remarkable annual growth rate of 60.58%, particularly evident over the past five years, the escalating volume of relevant publications reflects an expanding interest in the CE within the CDI and related supply chain subjects. This underscores academia’s pivotal role in advancing the transition toward a circular construction economy.Originality/valueThe study recommends refining CE strategies by exploring the circular design paradigms, optimizing supply chains, integrating digital technologies, establishing standardized metrics and scrutinizing CE’s impact within the CDI.