bluuebunny/crossref_metadata_2025_split huggingface dataset:
A challenging STEC strain isolation from patients’ stools: an O166:H15 STEC strain with the
stx2
gene
Authors: Thilakarathna Surangi H. , Li Vincent , Chui Linda 
Published: May 2024

ABSTRACT

Two patients with acute gastroenteritis tested positive for Shiga toxin-producing
Escherichia coli
(STEC) by polymerase chain reaction (PCR), and both strains carried the Shiga toxin 2 encoding gene. Since routine culture using CHROMagar STEC failed to recover these isolates, immunomagnetic separation (IMS) targeting the top six non-O157:H7 serotypes was used for isolate recovery. After two subsequent IMS runs, the STEC strains were isolated from trypticase soy broth with and without overnight enrichment for runs 1 and 2, respectively. Serotyping based on whole-genome sequencing revealed that both patients carried the strain O166:H15 STEC with the
stx2
gene. Hence, the magnetic beads used in IMS appeared to have cross-reactivity with other
E. coli
serotypes. When the STEC isolates from both stools were cultured on CHROMagar STEC and sheep blood agar (BAP), two distinct colony sizes were apparent after overnight incubation. The small and large colonies were picked and separately cultured on both media, and colony growth was observed for 2 weeks at room temperature after an initial overnight incubation at 37°C. After 1 week, the colonies showed concentric ring structures with a darker center and a lighter surrounding on CHROMagar STEC and a “fried egg”-resembling structure with a raised circular center and a flat surrounding on BAP. Both colony types remained morphologically different on CHROMagar STEC throughout the 15 days. However, on BAP, their appearance was comparable by day 7.

IMPORTANCE

Shiga toxin-producing
E. coli
(STEC) infections can lead to severe complications such as bloody diarrhea and hemolytic uremic syndrome (HUS), especially in young children and the elderly. Strains that carry the shiga toxin 2 gene (
stx2
), such as O157:H7, have been mostly linked with severe disease outcomes. In recent years, outbreaks caused by non-O157:H7 strains have increased.
E. coli
O166:H15 has been previously reported causing a gastroenteritis outbreak in 1996 as a non-STEC strain, however the O166:H15 serotype we recovered carried the
stx2
gene. It was particularly challenging to isolate this strain from stools by culture. Consequently, we tested immunomagnetic separation for the STEC recovery, which was a novel approach on clinical stools. Virulence genes were included for the characterization of these isolates.
The
Chlamydia trachomatis
Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners
Authors: Herrera Clara M. , McMahon Eleanor , Swaney Danielle L. , Sherry Jessica , Pha Khavong , Adams-Boone Kathleen , Johnson Jeffrey R. , Krogan Nevan J. , Stevers Meredith , Solomon David , Elwell Cherilyn , Engel Joanne 
Published: May 2024

ABSTRACT

Chlamydia trachomatis
is the leading cause of bacterial sexually transmitted infections in the USA and of preventable blindness worldwide. This obligate intracellular pathogen replicates within a membrane-bound inclusion, but how it acquires nutrients from the host while avoiding detection by the innate immune system is incompletely understood.
C. trachomatis
accomplishes this in part through the translocation of a unique set of effectors into the inclusion membrane, the
inc
lusion membrane proteins (Incs). Incs are ideally positioned at the host-pathogen interface to reprogram host signaling by redirecting proteins or organelles to the inclusion. Using a combination of co-affinity purification, immunofluorescence confocal imaging, and proteomics, we characterize the interaction between an early-expressed Inc of unknown function, Tri1, and tumor necrosis factor receptor-associated factor 7 (TRAF7). TRAF7 is a multi-domain protein with a RING finger ubiquitin ligase domain and a C-terminal WD40 domain. TRAF7 regulates several innate immune signaling pathways associated with
C. trachomatis
infection and is mutated in a subset of tumors. We demonstrate that Tri1 and TRAF7 specifically interact during infection and that TRAF7 is recruited to the inclusion. We further show that the predicted coiled-coil domain of Tri1 is necessary to interact with the TRAF7 WD40 domain. Finally, we demonstrate that Tri1 displaces the native TRAF7 binding partners, mitogen-activated protein kinase kinase kinase 2 (MEKK2), and MEKK3. Together, our results suggest that by displacing TRAF7 native binding partners, Tri1 has the capacity to alter TRAF7 signaling during
C. trachomatis
infection.

IMPORTANCE

Chlamydia trachomatis
is the leading cause of bacterial sexually transmitted infections in the USA and preventable blindness worldwide. Although easily treated with antibiotics, the vast majority of infections are asymptomatic and therefore go untreated, leading to infertility and blindness. This obligate intracellular pathogen evades the immune response, which contributes to these outcomes. Here, we characterize the interaction between a
C. trachomatis
-secreted effector, Tri1, and a host protein involved in innate immune signaling, TRAF7. We identified host proteins that bind to TRAF7 and demonstrated that Tri1 can displace these proteins upon binding to TRAF7. Remarkably, the region of TRAF7 to which these host proteins bind is often mutated in a subset of human tumors. Our work suggests a mechanism by which Tri1 may alter TRAF7 signaling and has implications not only in the pathogenesis of
C. trachomatis
infections but also in understanding the role of TRAF7 in cancer.
Paleontology, stratigraphy, and structural features of the lower bedded member of the Metaline Formation, Lafarge quarry, Metaline Falls, Washington, USA
Authors: Schofield* Glen J. , Pritchard Chad J. 
Published: May 2024

ABSTRACT
This one-day field trip of regional geologic significance goes from Spokane, Washington, north along the Pend Oreille River to the Lafarge limestone quarries in the Metaline Formation near Metaline Falls, Washington, USA. Along the way, we will discuss local geologic and geomorphic features, archaeology of the Native culture, features of Pleistocene glaciation and the Eocene Newport fault in the Pend Oreille valley, and highlights of roadcuts and rock types. The main focus of the field trip centers on the paleontology of the lower bedded member of the Metaline Formation in the Lafarge quarry. Based on recent fossil identification of recently discovered trilobites, the age of the lower bedded member has been refined to Series 2-Stage 4 of the Cambrian. We will examine potential new species at stopping points within the quarry, identify key units of stratigraphy and relate them to the stratigraphic column of the guide, and include a structural geology discussion. Deformed trilobites, cleavage, and calcite-filled fractures indicate NW-SE compression during Mesozoic Cordilleran tectonism.
Uncovering a Miocene forest in ancient Lake Clarkia and beyond
Authors: Love* Renee L. , MacKenzie* Lindsay , Spendlove* Ian 
Published: May 2024

ABSTRACT
The middle Miocene Clarkia Fossil Beds of northern Idaho, USA, is a world-renowned exceptional fossil deposit (Fossil-Lagerstätte). These ancient lake deposits contain fossils showing exceptional preservation of original plant material, insects, and fish, including organelles and possible ancient DNA, and their stable isotope signatures. Yang et al. (1995) determined the upper age of the lake deposits to be 15.78 ± 0.039 Ma during peak outflows of the Priest Rapids Member of the Wanapum Basalt of the Columbia River Basalt Group, part of Earth’s youngest large igneous province of continental flood basalts. The deposits capture a time in Earth’s history that represents our most recent major thermal optima, the Miocene Climatic Optimum, before the general decline in temperatures to the modern day. Nearby fossil sites, including the Oviatt Creek Fossil Beds and the Juliaetta Fossil Beds, record the persistence of the climatic optimum and subsequent cooling.
Conifers include Metasequoia (dawn redwood), Taxodium (bald cypress), Amentotaxus (Chinese yew), and Cunninghamia (Chinese fir). Angiosperm dicotyledon species also represent a much warmer climate than present day, including Cercidiphyllum (katsura), Zenia (Chinese legume), Zelkova (elm family), Magnolia (magnolia), Persea (avocado/bay family), Zizyphoides (buckthorn family), and Smilax (greenbriar). Estimates of the mean annual temperature from these fossil leaves range from 12° to 13 °C (53° to 55 °F). Mean annual precipitation values range from 200 to 216 cm/year with much higher humidity compared to today. Modern mean annual temperatures in northern Idaho are ~7 °C (47 °F), much cooler than Miocene temperatures. Today’s mean annual precipitation is estimated at ~80 cm/year. After the Miocene, many plant species representing mixed mesophytic broad-leaved forests started to disappear from the fossil record in North America and were thought to be extinct, only to be rediscovered in East Asia in more recent times (Cercidiphyllum, Cunninghamia, Metasequoia). This field trip will explore the Clarkia Fossil Beds and nearby fossil sites to examine the geology associated with the ancient lake and its fossils.
Handgrip strength and risks of diabetic vascular complications: Evidence from Guangzhou Diabetic Eye Study and UK cohorts
Authors: Zhong Pingting , Yang Shaopeng , Liu Riqian , Zhu Ziyu , Zhang Yongjie , Cheng Weijing , Wang Wei 
Published: May 2024

Purpose
The purpose is to investigate the association between handgrip strength (HGS) and the risk of future diabetic complications in multicountry cohorts.

Methods
The association between HGS and diabetic complications was evaluated using cox models among 84 453 patients with pre-diabetes and diabetes from the UK Biobank with a 12-year follow-up. The association between HGS and longitudinal microcirculatory damage rates was assessed among 819 patients with diabetes from the Guangzhou Diabetic Eye Study (GDES) with a 3-year follow-up. Participants were divided into three age groups (<56, 56–65 and ≥65 years), and each group was further subdivided into three HGS tertiles.

Results
A 5 kg reduction in HGS was associated with increased risk for all-cause mortality (women, HR=1.10, 95% CI: 1.05 to 1.14; p<0.001; men, HR=1.13, 95% CI: 1.11 to 1.15; p<0.001). Women and men in the lowest HGS group exhibited 1.6-times and 1.3–1.5-times higher risk of myocardial infarction and stroke compared with the highest HGS group. In men, there was a higher risk of developing end-stage renal disease (HR=1.83, 95% CI: 1.30 to 2.57; p=0.001), while this was not observed in women. Both sexes in the lowest HGS group had a 1.3-times higher risk of diabetic retinopathy compared with the highest HGS group. In the GDES group, individuals with the lowest HGS showed accelerated microcirculatory damage in retina (all p<0.05).

Conclusions
Reduced HGS is significantly associated with a higher risk of diabetic complications and accelerated microvascular damage. HGS could serve as a practical indicator of vascular health in patients with pre-diabetes and diabetes.
Clinical dimensions of people with co-occurring obsessive-compulsive and related disorders and multiple sclerosis: a scoping review protocol
Authors: Freedman David Eli , Sawicka Katherine M , Oh Jiwon , Main Emilia , Campbell Karen A , Feinstein Anthony 
Published: May 2024

IntroductionMultiple sclerosis (MS) is an immune-mediated demyelinating disease with a significant burden of neuropsychiatric sequelae. These symptoms, including depression and anxiety, are predictors of morbidity and mortality in people with MS. Despite a high prevalence of obsessive-compulsive disorder in MS, potentially shared pathophysiological mechanisms and overlap in possible treatments, no review has specifically examined the clinical dimensions of people with obsessive-compulsive and related disorders (OCRD) and MS. In this scoping review, we aim to map the available knowledge on the clinical dimensions of people with co-occurring OCRD and MS. Understanding the characteristics of this population in greater detail will inform more patient-centred care and create a framework for future studies.Methods and analysisWe developed a search strategy to identify all articles that include people with co-occurring OCRD and MS. The search strategy (extending to the grey literature) was applied to MEDLINE, Embase, PsycINFO, Cochrane Central Register of Controlled Trials, CINAHL, Web of Science and ProQuest Dissertations & Theses. Records will undergo title and abstract screening by two independent reviewers. Articles meeting inclusion criteria based on title and abstract screening will go on to full-text review by the two independent reviewers. After reaching a consensus about articles for inclusion in the final review, data will be extracted using a standardised extraction form. The extracted data will include clinical characteristics of patients such as age, gender, medication use and severity of MS, among others.Ethics and disseminationThis scoping review does not require research ethics approval. Results will be shared at national and/or international conferences, in a peer-reviewed journal publication, in a plain language summary and in a webinar for the general public.
Effects of primary or secondary prevention with vitamin A supplementation on clinically important outcomes: a systematic review of randomised clinical trials with meta-analysis and trial sequential analysis
Authors: Bjelakovic Goran , Nikolova Dimitrinka , Bjelakovic Milica , Pavlov Chavdar S , Sethi Naqash J , Korang Steven Kwasi , Gluud Christian 
Published: May 2024

ObjectivesThis systematic review with meta-analyses of randomised trials evaluated the preventive effects of vitamin A supplements versus placebo or no intervention on clinically important outcomes, in people of any age.MethodsWe searched different electronic databases and other resources for randomised clinical trials that had compared vitamin A supplements versus placebo or no intervention (last search 16 April 2024). We used Cochrane methodology. We used the random-effects model to calculate risk ratios (RRs), with 95% CIs. We analysed individually and cluster randomised trials separately. Our primary outcomes were mortality, adverse events and quality of life. We assessed risks of bias in the trials and used Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) to assess the certainty of the evidence.ResultsWe included 120 randomised trials (1 671 672 participants); 105 trials allocated individuals and 15 allocated clusters. 92 trials included children (78 individually; 14 cluster randomised) and 28 adults (27 individually; 1 cluster randomised). 14/105 individually randomised trials (13%) and none of the cluster randomised trials were at overall low risk of bias. Vitamin A did not reduce mortality in individually randomised trials (RR 0.99, 95% CI 0.93 to 1.05; I²=32%; p=0.19; 105 trials; moderate certainty), and this effect was not affected by the risk of bias. In individually randomised trials, vitamin A had no effect on mortality in children (RR 0.96, 95% CI 0.88 to 1.04; I²=24%; p=0.28; 78 trials, 178 094 participants) nor in adults (RR 1.04, 95% CI 0.97 to 1.13; I²=24%; p=0.27; 27 trials, 61 880 participants). Vitamin A reduced mortality in the cluster randomised trials (0.84, 95% CI 0.76 to 0.93; I²=66%; p=0.0008; 15 trials, 14 in children and 1 in adults; 364 343 participants; very low certainty). No trial reported serious adverse events or quality of life. Vitamin A slightly increased bulging fontanelle of neonates and infants. We are uncertain whether vitamin A influences blindness under the conditions examined.ConclusionsBased on moderate certainty of evidence, vitamin A had no effect on mortality in the individually randomised trials. Very low certainty evidence obtained from cluster randomised trials suggested a beneficial effect of vitamin A on mortality. If preventive vitamin A programmes are to be continued, supporting evidence should come from randomised trials allocating individuals and assessing patient-meaningful outcomes.PROSPERO registration numberCRD42018104347.
Light exposure profiles differ between myopes and non-myopes outside school hours
Authors: Dhakal Rohit , Lawrenson John G , Huntjens Byki , Shah Rakhee , Verkicharla Pavan Kumar 
Published: May 2024

PurposeConsidering the putative role of light in myopia, and variations in socioeconomic, lifestyle, educational and environmental factors across ethnicities, we objectively investigated light exposure patterns in Indian school children.MethodsThe light exposure profile of 143 school children (9–15 years, 50 myopes) recorded using a validated wearable light tracker for six continuous days was analysed. Additional data for non-school days were available for 87 children (26 myopes). The illuminance exposure levels, time spent outdoors and epoch (number of times participant is exposed to a predefined range of lux level per day) were compared between myopes and non-myopes across different light conditions: ≥1000, ≥3000, ≥5000 and ≥10 000 lux. For school days, light exposure profiles during (1) before school, school and after school hours; and (2) class, break and transition (when a student travels to and from school) time were analysed.ResultsThe overall median (IQR) daily illuminance exposure level, time spent outdoors and epochs at outdoors (≥1000 lux) were 807 (507–1079) lux/day, 46 (30–64) min/day and 9 (6–12) times/day, respectively. The daily illuminance exposure on non-school days was significantly higher in non-myopes than myopes (6369 (4508–9112) vs 5623 (2616–6929) lux/day, p=0.04). During transition time (school days), non-myopes had significantly higher illuminance exposure (910 (388–1479) vs 550 (263–1098) lux/day, p=0.04), spent more time outdoors (25 (10–43) vs 14 (4–29) min/day, p=0.01) and had higher outdoor epochs (6 (4–11) vs 5 (2–8) times/day, p=0.01) than myopes.ConclusionsA small but significant difference in illuminance exposure, time spent outdoors and epoch was noted between myopes and non-myopes during transition time, which may have implications in myopia control.
Interactions between LAMP3+ dendritic cells and T-cell subpopulations promote immune evasion in papillary thyroid carcinoma
Authors: Wang Zhiyuan , Ji Xiaoyu , Zhang Ye , Yang Fan , Su Hongyue , Zhang Hao , Li Zhendong , Zhang Wenqian , Sun Wei 
Published: May 2024

BackgroundThe incidence of papillary thyroid cancer (PTC) continues to rise all over the world, 10–15% of the patients have a poor prognosis. Although immunotherapy has been applied in clinical practice, its therapeutic efficacy remains far from satisfactory, necessitating further investigation of the mechanism of PTC immune remodeling and exploration of novel treatment targets.MethodsThis study conducted a single-cell RNA sequencing (scRNA-seq) analysis using 18 surgical tissue specimens procured from 14 patients diagnosed with adjacent tissues, non-progressive PTC or progressive PTC. Key findings were authenticated through spatial transcriptomics RNA sequencing, immunohistochemistry, multiplex immunohistochemistry, and an independent bulk RNA-seq data set containing 502 samples.ResultsA total of 151,238 individual cells derived from 18 adjacent tissues, non-progressive PTC and progressive PTC specimens underwent scRNA-seq analysis. We found that progressive PTC exhibits the following characteristics: a significant decrease in overall immune cells, enhanced immune evasion of tumor cells, and disrupted antigen presentation function. Moreover, we identified a subpopulation of lysosomal associated membrane protein 3 (LAMP3+) dendritic cells (DCs) exhibiting heightened infiltration in progressive PTC and associated with advanced T stage and poor prognosis of PTC. LAMP3+DCs promote CD8+T cells exhaustion (mediated by NECTIN2-TIGIT) and increase infiltration abundance of regulatory T cells (mediated by chemokine (C-C motif) ligand 17 (CCL17)-chemokine (C-C motif) receptor 4 (CCR4)) establishing an immune-suppressive microenvironment. Ultimately, we unveiled that progressive PTC tumor cells facilitate the retention of LAMP3+DCs within the tumor microenvironment through NECTIN3-NECTIN2 interactions, thereby rendering tumor cells more susceptible to immune evasion.ConclusionOur findings expound valuable insights into the role of the interaction between LAMP3+DCs and T-cell subpopulations and offer new and effective ideas and strategies for immunotherapy in patients with progressive PTC.
Intracranial thrombus composition is associated with occlusion location and endovascular treatment outcomes: results from ITACAT multicenter study
Authors: Juega Jesus , Requena Manuel , Piñana Carlos , Rodriguez Maite , Camacho Jessica , Vidal Marta , Moliné Teresa , Serna Garazi , Palacio-Garcia Carlos , Rubiera Marta , Garcia-Tornel Alvaro , Rodriguez-Villatoro Noelia , Rodriguez-Luna David , Muchada Marian , Olive Gadea Marta , Rizzo Federica , Rodrigo-Gisbert Marc , Lazaro Carlos , Hernandez David , de Dios Lascuevas Marta , Diana Francesco , Dorado Laura , Hernández-Pérez María , Quesada Helena , Cardona Portela Pere , De La Torre Carolina , Ramon-y-Cajal Santiago , Tomasello Alejandro , Ribo Marc , Molina Carlos A , Pagola Jorge 
Published: May 2024

BackgroundThe impact of thrombolytics directed towards different thrombus components regarding site of occlusion in combination with mechanical thrombectomy (MT) to achieve endovascular complete recanalization is unclear.MethodsRetrospective analysis of a prospective database in two stroke centers. Intracranial thrombi retrieved by MT were analyzed using hematoxylin–eosin staining for fibrin and red blood cell proportions, and CD61 immunostaining for platelets proportion in thrombus (PLTPT) assessment. Thrombi composition, baseline variables, etiology, treatment features and occlusion location were analyzed.ResultsOverall, 221 patients completed the per protocol analysis and 110 cases achieved a final expanded Thrombolysis in Cerebral Infarction (eTICI) 3 (49%) of which 70 were MT (32%) by first pass effect (FPE). Thrombi from medium distal vessel occlusions had higher PLTPT compared with thrombi from proximal large vessel occlusions (68% vs 61%, P=0.026). In particular, middle cerebral artery M2–M3 segment thrombi had the highest PLTPT (70%), and basilar artery thrombi the lowest PLTPT (41%). After logistic regression analysis adjusted for occlusion location and intravenous fibrinolysis, lower baseline National Institutes of Health Stroke Scale score (adjusted OR (aOR) 0.95, 95% CI 0.913 to 0.998) and PLTPT (aOR 0.97, 95% CI 0.963 to 0.993) were independently associated with FPE. Fewer MT passes (aOR 0.67, 95% CI 0.538 to 0.842) and platelet poor thrombus (<62% PLTPT; aOR 2.39, 95% CI 1.288 to 4.440) were independently associated with final eTICI 3.ConclusionsOcclusion location might be a surrogate parameter for thrombus composition. Platelet poor clots and fewer MT passes were independently associated with complete endovascular recanalization. Clinical trials testing the benefits of combining selective intra-arterial platelet antagonists with MT to improve endovascular outcomes are warranted.