bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remodeling of the gastric environment in
Helicobacter pylori
-induced atrophic gastritis
Authors: Shuman Jennifer H. B. , Lin Aung Soe , Westland Mandy D. , Bryant Kaeli N. , Piazuelo M. Blanca , Reyzer Michelle L. , Judd Audra M. , McDonald W. Hayes , McClain Mark S. , Schey Kevin L. , Algood Holly M. S. , Cover Timothy L. 
Published: December 2023

ABSTRACT

Helicobacter pylori
colonization of the human stomach is a strong risk factor for gastric cancer. To investigate
H. pylori
-induced gastric molecular alterations, we used a Mongolian gerbil model of gastric carcinogenesis. Histologic evaluation revealed varying levels of atrophic gastritis (a premalignant condition characterized by parietal and chief cell loss) in
H. pylori
-infected animals, and transcriptional profiling revealed a loss of markers for these cell types. We then assessed the spatial distribution and relative abundance of proteins in the gastric tissues using imaging mass spectrometry and liquid chromatography with tandem mass spectrometry. We detected striking differences in the protein content of corpus and antrum tissues. Four hundred ninety-two proteins were preferentially localized to the corpus in uninfected animals. The abundance of 91 of these proteins was reduced in
H. pylori
-infected corpus tissues exhibiting atrophic gastritis compared with infected corpus tissues exhibiting non-atrophic gastritis or uninfected corpus tissues; these included numerous proteins with metabolic functions. Fifty proteins localized to the corpus in uninfected animals were diffusely delocalized throughout the stomach in infected tissues with atrophic gastritis; these included numerous proteins with roles in protein processing. The corresponding alterations were not detected in animals infected with a
H. pylori
∆
cagT
mutant (lacking Cag type IV secretion system activity). These results indicate that
H. pylori
can cause loss of proteins normally localized to the gastric corpus as well as diffuse delocalization of corpus-specific proteins, resulting in marked changes in the normal gastric molecular partitioning into distinct corpus and antrum regions.

IMPORTANCE

A normal stomach is organized into distinct regions known as the corpus and antrum, which have different functions, cell types, and gland architectures. Previous studies have primarily used histologic methods to differentiate these regions and detect
H. pylori
-induced alterations leading to stomach cancer. In this study, we investigated
H. pylori
-induced gastric molecular alterations in a Mongolian gerbil model of carcinogenesis. We report the detection of numerous proteins that are preferentially localized to the gastric corpus but not the antrum in a normal stomach. We show that stomachs with
H. pylori-
induced atrophic gastritis (a precancerous condition characterized by the loss of specialized cell types) exhibit marked changes in the abundance and localization of proteins normally localized to the gastric corpus. These results provide new insights into
H. pylori
-induced gastric molecular alterations that are associated with the development of stomach cancer.
Comparative evaluation of small molecules reported to be inhibitors of
Staphylococcus aureus
biofilm formation
Authors: Campbell Mara J. , Beenken Karen E. , Spencer Horace J. , Jayana Bina , Hester Hana , Sahukhal Gyan S. , Elasri Mohamed O. , Smeltzer Mark S. 
Published: December 2023

ABSTRACT

Biofilm formation is an important characteristic of many
Staphylococcus aureus
infections because it limits the efficacy of host defenses and conventional antibiotic therapy. There are many literature reports that describe small molecule inhibitors of
S. aureus
biofilm formation, but the lack of direct comparisons and differences in the methods used to assess inhibition make it impossible to assess the efficacy of these compounds relative to each other. To address this, we compared 19 compounds reported in the literature to be inhibitors of
S. aureus
biofilm formation. We used the methicillin-susceptible clinical osteomyelitis isolate UAMS-1 in a microtiter plate biofilm assay shown to maximize biofilm formation and provide results consistent with those observed
in vivo
. Under these conditions, telithromycin (Ketek) showed the greatest inhibitory activity, limiting biofilm formation to a degree comparable to a UAMS-1
sarA
mutant at a concentration of 0.49 µM (0.40 µg/mL). Similar results were obtained for the methicillin-resistant USA300 strain LAC. Telithromycin is a bacteriostatic ketolide antibiotic that is not currently approved in the United States for use as an antibiotic due to its concerning safety profile. However, the concentration required to limit growth
in vitro
was higher than the concentration required to limit biofilm formation, suggesting that low-dose telithromycin might be useful to limit biofilm formation and increase the efficacy of other antibiotics in biofilm-associated infections. Irrespective of whether telithromycin is ultimately proven clinically useful in this regard, these results emphasize the need for widespread use of a standardized
in vitro
approach to evaluate prospective inhibitors.

IMPORTANCE

Because biofilm formation is such a problematic feature of
Staphylococcus aureus
infections, much effort has been put into identifying biofilm inhibitors. However, the results observed with these compounds are often reported in isolation, and the methods used to assess biofilm formation vary between labs, making it impossible to assess relative efficacy and prioritize among these putative inhibitors for further study. The studies we report address this issue by directly comparing putative biofilm inhibitors using a consistent
in vitro
assay. This assay was previously shown to maximize biofilm formation, and the results observed with this assay have been proven to be relevant
in vivo
. Of the 19 compounds compared using this method, many had no impact on biofilm formation under these conditions. Indeed, only one proved effective at limiting biofilm formation without also inhibiting growth.
Multicomponent Synthesis of Pyridine and Pyrimidine Derivatives Initiated by the Knoevenagel Reaction
Authors: Dyachenko I. V. , Dyachenko V. D. , Dorovatovskii P. V. , Khrustalev V. N. , Nenajdenko V. G. 
Published: December 2023

Abstract
Multicomponent condensation of alkylating reagents with carbonyl compounds functionalized by CH-acids is initiated by the Knoevenagel reaction and leads to the formation of substituted pyridines, thienopyridines, pyridothienopyridines, and pyrimidothienopyridopyrimidines. The structure of the key products was studied by the X-ray diffraction method.
Insights for enhancing resilience in prolonged crises: impact of COVID-19 pandemic on nurses’ quality of life
Authors: Salimi Saleh , Özel Selman 
Published: December 2023

Aims and backgroundThe COVID-19 pandemic has had adverse effects on nurses, impacting them physically, mentally and psychosocially. These effects stem from heightened workloads, fears of contracting a life-threatening illness due to inadequate protective equipment and concerns about transmitting the disease to their families. This study assessed the impact of COVID-19 on the quality of life of nurses working on the frontlines, aiming to provide insights for future crisis responses.MethodsA descriptive-analytic study included 288 nurses from hospitals affiliated with Çukurova University, Southern Turkey using a stratified sampling method. Data on quality of life and demographics were collected using the WHO Quality of Life-BREF scale and a questionnaire. Data analysis was conducted using SPSS V.25, employing descriptive and analytic measures at a significance level of p<0.05.ResultsOverall perceived quality of life was moderate (mean score: 3.31; SD: 0.56), with the highest scores in social relationships, psychological well-being and environmental factors. Positive correlations were found with gender, education, salary, vaccination status and living alone. Negative correlations were observed with alcohol consumption and longer working hours.ConclusionsTo strengthen future crisis responses, health authorities should prioritise workload reduction, gender diversity promotion, support for nurses residing with family, better income opportunities, alcohol abstinence encouragement and ensuring vaccination for frontline nurses.
Bracing requirements and design for a single column considering semi-rigid connections and initial curvature
Authors: Zhang Linbo , Xu Lei 
Published: December 2023

The use of bracing has been widely recognized as an effective technique to increase the strength of columns by reducing their effective length. This paper presents an assessment of the bracing requirements for a semi-rigidly connected column, which is laterally braced at the mid-height. By utilizing the proposed half-length column model, the effects of column stiffness and initial curvature on the brace strength and stiffness requirements are investigated. The results indicate that the column’s initial curvature coefficient increases with a higher applied load, but decreases with increased column end connection stiffness. The required brace stiffness requirement stipulated in AISC 360-22 should be increased when considering the effect of column’s initial curvature. Following the design concepts of AISC 360-22 and CSA S16-19, equations for assessing the bracing requirements for a semi-rigidly connected column are proposed. These equations are validated against the finite element analysis results, demonstrating their ability to accurately assess the bracing requirements for semi-rigidly connected columns. These equations can be adopted in current engineering practice.
Induced phase transformation in ionizable colloidal nanoparticles
Authors: López-Flores Leticia , de la Cruz Monica Olvera 
Published: December 2023

Abstract
Acid–base equilibria directly influence the functionality and behavior of particles in a system. Due to the ionizing effects of acid–base functional groups, particles will undergo charge exchange. The degree of ionization and their intermolecular and electrostatic interactions are controlled by varying the pH and salt concentration of the solution in a system. Although the pH can be tuned in experiments, it is hard to model this effect using simulations or theoretical approaches. This is due to the difficulty in treating charge regulation and capturing the cooperative effects in a colloidal suspension with Coulombic interaction. In this work, we analyze a suspension of ionizable colloidal particles via molecular dynamics (MD) simulations, along with Monte Carlo simulations for charge regulation (MC-CR) and derive a phase diagram of the system as a function of pH. It is observed that as pH increases, particles functionalized with acid groups change their arrangement from face-centered cubic (FCC) packing to a disordered state. We attribute these transitions to an increase in the degree of charge polydispersity arising from an increase in pH. Our work shows that charge regulation leads to amorphous solids in colloids when the mean nanoparticle charge is sufficiently high.

Graphical abstract
Cretaceous stratigraphy of Antarctica and its global significance
Authors: Crame J. Alistair , Francis Jane E. 
Published: December 2023

Abstract
The Cretaceous Period is particularly well represented by a thick sequence of clastic sedimentary rocks exposed in the Antarctic Peninsula region of western Antarctica. This was an active margin throughout the Late Mesozoic, and in total some 7 km+ of Cretaceous sedimentary rocks accumulated in a series of fore-, intra- and back-arc basins. The Fossil Bluff Group of eastern Alexander Island can be traced from the Jurassic–Cretaceous boundary into the Upper Albian and represents a broad-scale shallowing-upward sequence from deep marine to a prominent Upper Albian fluvial interval in which high-density forests developed at a palaeolatitude of 75° S. The Cretaceous sequence exposed in the James Ross Island group continues right through the Upper Cretaceous to the Cretaceous–Paleogene boundary. The Campanian–Maastrichtian succession in particular is over 2 km in total thickness and richly fossiliferous. The improved Cretaceous stratigraphy of Antarctica is an invaluable terrestrial record of climatic change at a high palaeolatitude. This includes a gradual increase in temperature to the Cretaceous Thermal Maximum, and then a decline to the Cretaceous–Paleogene boundary. There may be no simple link between these palaeotemperature changes and Cretaceous patterns of biotic radiation and extinction.
Innate Lymphoid Cells in Bladder Cancer: From Mechanisms of Action to Immune Therapies
Authors: Noel Onika D.V. , Hassouneh Zaineb , Svatek Robert S. , Mukherjee Neelam 
Published: December 2023

AbstractBladder tumors have a high mutational burden and tend to be responsive to immune therapies; however, response rates remain modest. To date, immunotherapy in bladder cancer has largely focused on enhancing T-cell immune responses in the bladder tumor microenvironment. It is anticipated that other immune cells, including innate lymphoid cells (ILC), which play an important role in bladder oncogenesis and tumor suppression, could be targeted to improve response to existing therapies. ILCs are classified into five groups: natural killer cells, ILC1s, ILC2s, ILC3s, and lymphoid tissue inducer cells. ILCs are pleiotropic and play dual and sometimes paradoxical roles in cancer development and progression. Here, a comprehensive discussion of the current knowledge and recent advancements in understanding the role of ILCs in bladder cancer is provided. We discuss the multifaceted roles that ILCs play in bladder immune surveillance, tumor protection, and immunopathology of bladder cancer. This review provides a rationale for targeting ILCs in bladder cancer, which is relevant for other solid tumors.
Platelet RNA Biomarker of Ticagrelor-Responsive Genes Is Associated With Platelet Function and Cardiovascular Events
Authors: Myers Rachel A. , Ortel Thomas L. , Waldrop Alexander , Cornwell MacIntosh , Newman Jonathan D. , Levy Natalie K. , Barrett Tessa J. , Ruggles Kelly , Sowa Marcin A. , Dave Sandeep , Ginsburg Geoffrey S. , Berger Jeffrey S. , Voora Deepak 
Published: December 2023

BACKGROUND:
Identifying patients with the optimal risk:benefit for ticagrelor is challenging. The aim was to identify ticagrelor-responsive platelet transcripts as biomarkers of platelet function and cardiovascular risk.

METHODS:
Healthy volunteers (n=58, discovery; n=49, validation) were exposed to 4 weeks of ticagrelor with platelet RNA data, platelet function, and self-reported bleeding measured pre-/post-ticagrelor. RNA sequencing was used to discover platelet genes affected by ticagrelor, and a subset of the most informative was summarized into a composite score and tested for validation. This score was further analyzed (1) in CD34+ megakaryocytes exposed to an P2Y12 inhibitor in vitro, (2) with baseline platelet function in healthy controls, (3) in peripheral artery disease patients (n=139) versus patient controls (n=30) without atherosclerosis, and (4) in patients with peripheral artery disease for correlation with atherosclerosis severity and risk of incident major adverse cardiovascular and limb events.

RESULTS:
Ticagrelor exposure differentially expressed 3409 platelet transcripts. Of these, 111 were prioritized to calculate a Ticagrelor Exposure Signature score, which ticagrelor reproducibly increased in discovery and validation cohorts. Ticagrelor’s effects on platelets transcripts positively correlated with effects of P2Y12 inhibition in primary megakaryocytes. In healthy controls, higher baseline scores correlated with lower baseline platelet function and with minor bleeding while receiving ticagrelor. In patients, lower scores independently associated with both the presence and extent of atherosclerosis and incident ischemic events.

CONCLUSIONS:
Ticagrelor-responsive platelet transcripts are a biomarker for platelet function and cardiovascular risk and may have clinical utility for selecting patients with optimal risk:benefit for ticagrelor use.
Thrombomodulin Regulates PTEN/AKT Signaling Axis in Endothelial Cells
Authors: Giri Hemant , Biswas Indranil , Rezaie Alireza R. 
Published: December 2023

BACKGROUND:

We recently demonstrated that deletion of thrombomodulin gene from endothelial cells results in upregulation of proinflammatory phenotype. In this study, we investigated the molecular basis for the altered phenotype in thrombomodulin-deficient (TM
−/−
) cells.

METHODS:

Different constructs containing deletions or mutations in the cytoplasmic domain of thrombomodulin were prepared and introduced to TM
−/−
cells. The phenotype of cells expressing different derivatives of thrombomodulin and tissue samples of thrombomodulin-knockout mice were analyzed for expression of distinct regulatory genes in established signaling assays.

RESULTS:

The phosphatase and tensin homolog were phosphorylated and its recruitment to the plasma membrane was impaired in TM
−/−
cells, leading to hyperactivation of AKT (protein kinase B) and phosphorylation-dependent nuclear exclusion of the transcription factor, forkhead box O1. The proliferative/migratory properties of TM
−/−
cells were enhanced, and cells exhibited hypersensitivity to stimulation by angiopoietin 1 and vascular endothelial growth factor. Reexpression of wild-type thrombomodulin in TM
−/−
cells normalized the cellular phenotype; however, thrombomodulin lacking its cytoplasmic domain failed to restore the normal phenotype in TM
−/−
cells. Increased basal permeability and loss of VE-cadherin were restored to normal levels by reexpression of wild-type thrombomodulin but not by a thrombomodulin construct lacking its cytoplasmic domain. A thrombomodulin cytoplasmic domain deletion mutant containing 3-membrane-proximal Arg-Lys-Lys residues restored the barrier-permeability function of TM
−/−
cells. Enhanced phosphatase and tensin homolog phosphorylation and activation of AKT and mTORC1 (mammalian target of rapamycin complex 1) were also observed in the liver of thrombomodulin-KO mice.

CONCLUSIONS:
These results suggest that the cytoplasmic domain of thrombomodulin interacts with the actin cytoskeleton and plays a crucial role in regulation of phosphatase and tensin homolog/AKT signaling in endothelial cells.
My Big, Fat 50-Year Journey
Authors: Palmer Martha 
Published: December 2023

Abstract
My most heartfelt thanks to ACL for this tremendous honor. I’m completely thrilled. I cannot tell you how surprised I was when I got Iryna’s email. It is amazing that my first ACL conference since 2019 in Florence includes this award. What a wonderful way to be back with all of my friends and family here at ACL. I’m going to tell you about my big fat 50-year journey. What have I been doing for the last 50 years? Well, finding meaning, quite literally in words. Or in other words, exploring how computational lexical semantics can support natural language understanding. This is going to be quick. Hold onto your hats, here we go.
Updates in Bariatric Surgery
Authors: Hsu Justin L. , Farrell Timothy M. 
Published: December 2023

Bariatric surgery is currently the most effective long-term treatment for morbid obesity as well as type-2 diabetes mellitus. The field of metabolic and bariatric surgery has seen tremendous growth over the past decade with dramatically reduced risks. This article aims to provide an update on bariatric surgery, highlighting the latest outcomes, improvements, and challenges in the field. Recently, the American Society of Metabolic and Bariatric Surgery (ASMBS) and the International Federation for the Surgery of Obesity and Metabolic Disorders (IFSO) released a major update to the indications for bariatric surgery at BMI ≥35 kg/m2 regardless of co-morbidities and 30-34.9 kg/m2 with obesity-related comorbidities. Sleeve gastrectomy has emerged as the most popular bariatric procedure in the last 10 years with its remarkable efficacy and safety profile. The implementation of the Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) and Enhanced Recovery After Surgery (ERAS) protocols have significantly improved the quality of care for all bariatric patients. The recent introduction and FDA approval of Glucagon-Like Peptide-1 (GLP-1) agonists for chronic obesity has garnered significant media coverage and popularity, but no guidelines exist regarding its use in relation to bariatric surgery. This update underscores the need for tailored approaches, ongoing research, and the integration of evidence-based medicine and innovations to enhance patient care.
Clinical Surveillance vs Anticoagulation Therapy for Isolated Subsegmental Pulmonary Embolism: A Systematic Review of Clinical Outcomes
Authors: Chin Brian , Tweedie Caitlin , Nasef Hazem , Hernandez Nickolas , Wright D-Dre , Awan Muhammad Usman , Elkbuli Adel 
Published: December 2023

Background This systematic review aims to evaluate and compare differences in clinical outcomes for adult patients diagnosed with ISSPE who were managed with anticoagulation vs clinical surveillance. Methods PubMed, Embase, ProQuest, Cochrane, and Google Scholar were searched to identify studies evaluating the use of anticoagulation and/or clinical surveillance in patients diagnosed with ISSPE. The search included studies published up to August 3, 2023. Outcomes of interest included 90-day recurrent venous thromboembolism (VTE), major bleeding, and all-cause mortality rates. Results Ten studies were included with a total of 1224 patients. Of these patients, 791 were treated with anticoagulation and 433 underwent surveillance. Studies found no difference in recurrent VTE rates, with the majority of studies reporting no recurrence. Of the studies that reported VTE recurrence, rates were .5% to 1.4% for the anticoagulation groups and 3.1% to 3.2% for the surveillance groups. Major bleeding rates were also similar. In anticoagulated patients, major bleeding rates ranged from 1% to 10%. In clinical surveillance patients, the majority found no rate of major bleeding, with 2 studies reporting rates of .8% to 3.2%. Mortality rates ranged widely with no significant differences reported. Conclusion Clinical surveillance appears to be a safe and effective alternative to anticoagulation in patients with ISSPE. Ninety-day rates of recurrent VTE, major bleeding, and mortality were comparable between groups. These findings highlight the need for updated practice management guidelines to improve patient outcomes.