bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surge effects and survival to hospital discharge in critical care patients with COVID-19 during the early pandemic: a cohort study
Authors: Dale Christopher R. , Starcher Rachael W. , Chang Shu Ching , Robicsek Ari , Parsons Guilford , Goldman Jason D. , Vovan Andre , Hotchkin David , Gluckman Tyler J. 
Published: February 2021

Abstract
Background
The early months of the COVID-19 pandemic were fraught with much uncertainty and some resource constraint. We assessed the change in survival to hospital discharge over time for intensive care unit patients with COVID-19 during the first 3 months of the pandemic and the presence of any surge effects on patient outcomes.

Methods
Retrospective cohort study using electronic medical record data for all patients with laboratory-confirmed COVID-19 admitted to intensive care units from February 25, 2020, to May 15, 2020, at one of 26 hospitals within an integrated delivery system in the Western USA. Patient demographics, comorbidities, and severity of illness were measured along with medical therapies and hospital outcomes over time. Multivariable logistic regression models were constructed to assess temporal changes in survival to hospital discharge during the study period.

Results
Of 620 patients with COVID-19 admitted to the ICU [mean age 63.5 years (SD 15.7) and 69% male], 403 (65%) survived to hospital discharge and 217 (35%) died in the hospital. Survival to hospital discharge increased over time, from 60.0% in the first 2 weeks of the study period to 67.6% in the last 2 weeks. In a multivariable logistic regression analysis, the risk-adjusted odds of survival to hospital discharge increased over time (biweekly change, adjusted odds ratio [aOR] 1.22, 95% CI 1.04–1.40, P = 0.02). Additionally, an a priori-defined explanatory model showed that after adjusting for both hospital occupancy and percent hospital capacity by COVID-19-positive individuals and persons under investigation (PUI), the temporal trend in risk-adjusted patient survival to hospital discharge remained the same (biweekly change, aOR 1.18, 95% CI 1.00–1.38, P = 0.04). The presence of greater rates of COVID-19 positive/PUI as a percentage of hospital capacity was, however, significantly and inversely associated with survival to hospital discharge (aOR 0.95, 95% CI 0.92–0.98, P < 0.01).

Conclusions
During the early COVID-19 pandemic, risk-adjusted survival to hospital discharge increased over time for critical care patients. An association was also seen between a greater COVID-19-positive/PUI percentage of hospital capacity and a lower survival rate to hospital discharge.
FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants
Authors: Long Yanping , Liu Zhijian , Jia Jinbu , Mo Weipeng , Fang Liang , Lu Dongdong , Liu Bo , Zhang Hong , Chen Wei , Zhai Jixian 
Published: February 2021

AbstractThe broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities.
In situ measurements of oxidation–reduction potential and hydrogen peroxide concentration as tools for revealing LPMO inactivation during enzymatic saccharification of cellulose
Authors: Kadić Adnan , Várnai Anikó , Eijsink Vincent G. H. , Horn Svein Jarle , Lidén Gunnar 
Published: February 2021

Abstract
Background
Biochemical conversion of lignocellulosic biomass to simple sugars at commercial scale is hampered by the high cost of saccharifying enzymes. Lytic polysaccharide monooxygenases (LPMOs) may hold the key to overcome economic barriers. Recent studies have shown that controlled activation of LPMOs by a continuous H2O2 supply can boost saccharification yields, while overdosing H2O2 may lead to enzyme inactivation and reduce overall sugar yields. While following LPMO action by ex situ analysis of LPMO products confirms enzyme inactivation, currently no preventive measures are available to intervene before complete inactivation.

Results
Here, we carried out enzymatic saccharification of the model cellulose Avicel with an LPMO-containing enzyme preparation (Cellic CTec3) and H2O2 feed at 1 L bioreactor scale and followed the oxidation–reduction potential and H2O2 concentration in situ with corresponding electrode probes. The rate of oxidation of the reductant as well as the estimation of the amount of H2O2 consumed by LPMOs indicate that, in addition to oxidative depolymerization of cellulose, LPMOs consume H2O2 in a futile non-catalytic cycle, and that inactivation of LPMOs happens gradually and starts long before the accumulation of LPMO-generated oxidative products comes to a halt.

Conclusion
Our results indicate that, in this model system, the collapse of the LPMO-catalyzed reaction may be predicted by the rate of oxidation of the reductant, the accumulation of H2O2 in the reactor or, indirectly, by a clear increase in the oxidation–reduction potential. Being able to monitor the state of the LPMO activity in situ may help maximizing the benefit of LPMO action during saccharification. Overcoming enzyme inactivation could allow improving overall saccharification yields beyond the state of the art while lowering LPMO and, potentially, cellulase loads, both of which would have beneficial consequences on process economics.
Lymphatic muscle cells contribute to dysfunction of the synovial lymphatic system in inflammatory arthritis in mice
Authors: Liang Qianqian , Zhang Li , Xu Hao , Li Jinlong , Chen Yan , Schwarz Edward M. , Shi Qi , Wang Yongjun , Xing Lianping 
Published: February 2021

AbstractBackgroundOur previous studies reveal that impaired draining function of the synovial lymphatic vessel (LV) contributes to the pathogenesis of inflammatory arthritis, but the cellular and molecular mechanisms involved are not fully understood.ObjectiveTo investigate the involvement of lymphatic muscle cells (LMCs) in mediating impaired LV function in inflammatory arthritis.MethodsTNF transgenic (TNF-Tg) arthritic mice were used. The structure and function of the LVs that drained the hind limbs were examined by whole-mount immunofluorescence staining, electron microscopy, and near-infrared lymphatic imaging. Primary LMCs were treated with TNF, and the changes in proliferation, apoptosis, and functional gene expression were assessed. The roles of the herbal drug, Panax notoginseng saponins (PNS), in arthritis and LVs were studied.ResultsTNF-Tg mice developed ankle arthritis with age, which was associated with abnormalities of LVs: (1) dilated capillary LVs with few branch points, (2) mature LVs with reduced LMC coverage and draining function, and (3) degenerative and apoptotic appearance of LMCs. TNF caused LMC apoptosis, reduced expression of muscle functional genes, and promoted the production of nitric oxide (NO) by lymphatic endothelial cells (LECs). PNS attenuated arthritis, restored LMC coverage and draining function of mature LVs, inhibited TNF-mediated NO expression, and reduced LMC apoptosis.ConclusionThe impaired draining function of LVs in TNF-Tg mice involves LMC apoptosis. TNF promotes LMC death directly and indirectly via NO production by LECs. PNS attenuates arthritis, improves LVs, and prevents TNF-induced LMC apoptosis by inhibiting NO production of LECs. LMCs contribute to the dysfunction of synovial LVs in inflammatory arthritis.
The effect of pelvic pathology on uterine vein diameters
Authors: Amin T. N. , Wong M. , Foo X. , Pointer S.-L. , Goodhart V. , Jurkovic D. 
Published: February 2021

Abstract
Background
Transvaginal ultrasound (TVS) is a sensitive tool for detecting various conditions that contribute to pelvic pain. TVS can be also used to assess blood flow and measure the size of pelvic veins. Pelvic venous congestion (PVC) is characterised by enlargement of the pelvic veins and has been recognised as a cause of chronic pelvic pain. The reference ranges for uterine venous diameter in women with normal pelvic organs have been established, but there is no information regarding the potential effect of pelvic pathology on the uterine venous diameters. The aim of this study was to examine the size of uterine venous plexus in women with evidence of pelvic abnormalities on TVS and to determine whether the reference ranges need to be adjusted in the presence of pelvic pathology.
A prospective, observational study was conducted in our gynaecological outpatient clinic. Morphological characteristics of all pelvic abnormalities detected on TVS and their sizes were recorded. The uterine veins were identified and their diameters were measured in all cases. The primary outcome measure was the uterine venous diameter. Regression analyses were performed to determine factors affecting the uterine venous size in women with pelvic pathology.

Results
A total of 1500 women were included into the study, 1014 (67%) of whom were diagnosed with pelvic abnormalities. Women with pelvic pathology had significantly larger uterine venous diameters than women with normal pelvic organs (p < 0.01). Multivariable analysis showed that pre-menopausal status, high parity, presence of fibroids (p < 0.001) and Black ethnicity were all associated with significantly larger uterine vein diameters. Based on these findings modified reference ranges for uterine venous diameters have been designed which could be used for the diagnosis of PVC in women with uterine fibroids.

Conclusions
Our findings show that of all pelvic pathology detected on TVS, only fibroids are significantly associated with uterine venous enlargement. Factors known to be associated with enlarged veins in women with normal pelvic organs, namely parity and menopausal status, also apply in patients with pelvic pathology. Future studies of uterine venous circulation should take into account the presence and size of uterine fibroids when assessing women for the signs of PVC.
Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors
Authors: Sarhadi Virinder , Mathew Binu , Kokkola Arto , Karla Tiina , Tikkanen Milja , Rautelin Hilpi , Lahti Leo , Puolakkainen Pauli , Knuutila Sakari 
Published: February 2021

AbstractBackgroundGastric adenocarcinoma is associated withH. pyloriinfection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls.ResultsWe found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance ofEnterobacteriaceaewas observed in both adenocarcinoma subtypes, whereas lower abundance ofBifidobacteriaceaewas seen only in diffuse adenocarcinoma and ofOscillibacterin intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance ofEnterobacteriaceaeand lower abundance ofLactobacillaceaeandOscillibacterwhile lower abundance ofLachnoclostridium, Bifidobacterium, ParabacteroidesandBarnesiellawas seen only in the adenocarcinoma patients.ConclusionsOur analysis shows association of higherEnterobacteriaceaeabundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.
Data on gender representation in food and beverage print advertisements found in corner stores from Guatemala and Peru
Authors: Rozas Lucila , Busse Peter , Barnoya Joaquin , Garrón Alejandra 
Published: February 2021

Abstract
Objectives
Data on gender representation in food and beverage advertisements may allow for a better understanding of how the food industry is targeting different audiences based on gender. Nonetheless, scant research on food and beverage print advertising with a gender approach has been conducted. Therefore, we sought to assess the prevalence of gender focus in print advertisements found inside corner stores in two cities: Guatemala City, Guatemala, and Lima, Peru.

Data description
We developed two complementary datasets as part of the study: (1) a dataset of digital photographs of 200 food and beverage print advertisements found in corner stores located near schools (100 ads per country selected according to criteria such as product type, image quality, and uniqueness); (2) a quantitative dataset with data of the content analysis of these photographs. We employed 19 variables to record the general information and gender assessment of the ads. These datasets should allow scholars and public officials to identify gender-specific marketing strategies of the food industry that might impact children’s and adolescents’ nutrition differently.
MicroRNAs overexpressed in Crohn’s disease and their interactions with mechanisms of epigenetic regulation explain novel aspects of Crohn’s disease pathogenesis
Authors: Fernández-Ponce Cecilia , Navarro Quiroz Roberto , Díaz Perez Anderson , Aroca Martinez Gustavo , Cadena Bonfanti Andrés , Acosta Hoyos Antonio , Gómez Escorcia Lorena , Hernández Agudelo Sandra , Orozco Sánchez Christian , Villarreal Camacho José , Atencio Ibarra Linda , Consuegra Machado Jose , Espinoza Garavito Alberto , García-Cózar Francisco , Navarro Quiroz Elkin 
Published: February 2021

Abstract
Background
In this review, we were interested to identify the wide universe of enzymes associated with epigenetic modifications, whose gene expression is regulated by miRNAs with a high relative abundance in Crohn's disease (CD) affected tissues, with the aim to determine their impact in the pathogenesis and evolution of the disease.

Methods
We used HMDD and Bibliometrix R-package in order to identify the miRNAs overexpressed in CD. The identified enzymes associated with epigenetic mechanisms and post-translational modifications, regulated by miRNAs upregulated in CD, were analyzed using String v11 database.

Results
We found 190 miRNAs with great abundance in patients with CD, of which 26 miRNAs regulate the gene expression of enzymes known to catalyze epigenetic modifications involved in essentials pathophysiological processes, such as chromatin architecture reorganization, immune response regulation including CD4+ T cells polarization, integrity of gut mucosa, gut microbiota composition and tumorigenesis.

Conclusion
The integrated analysis of miRNAs with a high relative abundance in patients with CD showed a combined and superimposed gene expression regulation of enzymes associated with relevant epigenetic mechanisms and that could explain, in part, the pathogenesis of CD.
Cognitive trajectories of patients with focal ß-amyloid deposition
Authors: Kim Si Eun , Lee Byungju , Jang Hyemin , Chin Juhee , Khoo Ching Soong , Choe Yeong Sim , Kim Ji Sun , Kang Sung Hoon , Kim Hang-Rai , Hwangbo Song , Jeong Jee Hyang , Yoon Soo Jin , Park Kyung Won , Kim Eun-Joo , Yoon Bora , Jang Jae-Won , Hong Jin Yong , Na Duk L. , Seo Sang Won , Choi Seong Hye , Kim Hee Jin 
Published: February 2021

Abstract
Background
The presence of ß-amyloid (Aß) in the brain can be identified using amyloid PET. In clinical practice, the amyloid PET is interpreted based on dichotomous visual rating, which renders focal Aß accumulation be read as positive for Aß. However, the prognosis of patients with focal Aß deposition is not well established. Thus, we investigated cognitive trajectories of patients with focal Aß deposition.

Methods
We followed up 240 participants (112 cognitively unimpaired [CU], 78 amnestic mild cognitive impairment [aMCI], and 50 Alzheimer’s disease (AD) dementia [ADD]) for 2 years from 9 referral centers in South Korea. Participants were assessed with neuropsychological tests and 18F-flutemetamol (FMM) positron emission tomography (PET). Ten regions (frontal, precuneus/posterior cingulate (PPC), lateral temporal, parietal, and striatum of each hemisphere) were visually examined in the FMM scan, and participants were divided into three groups: No-FMM, Focal-FMM (FMM uptake in 1–9 regions), and Diffuse-FMM. We used mixed-effects model to investigate the speed of cognitive decline in the Focal-FMM group according to the cognitive level, extent, and location of Aß involvement, in comparison with the No- or Diffuse-FMM group.

Results
Forty-five of 240 (18.8%) individuals were categorized as Focal-FMM. The rate of cognitive decline in the Focal-FMM group was faster than the No-FMM group (especially in the CU and aMCI stage) and slower than the Diffuse-FMM group (in particular in the CU stage). Within the Focal-FMM group, participants with FMM uptake to a larger extent (7–9 regions) showed faster cognitive decline compared to those with uptake to a smaller extent (1–3 or 4–6 regions). The Focal-FMM group was found to have faster cognitive decline in comparison with the No-FMM when there was uptake in the PPC, striatum, and frontal cortex.

Conclusions
When predicting cognitive decline of patients with focal Aß deposition, the patients’ cognitive level, extent, and location of the focal involvement are important.
ARID1A genomic alterations driving microsatellite instability through somatic MLH1 methylation with response to immunotherapy in metastatic lung adenocarcinoma: a case report
Authors: Durán Mercedes , Faull Iris , Lastra Enrique , Laes Jean-Francois , Rodrigo Ana Belén , Sánchez-Escribano Ricardo 
Published: February 2021

Abstract
Background
Tumor molecular screening allows categorization of molecular alterations to select the best therapeutic strategy. AT-rich interactive domain-containing 1A (ARID1A) gene mutations are present in gastric, endometrial, and clear cell ovarian tumors. Inactivation of this gene impairs mismatch repair (MMR) machinery leading to an increased mutation burden that correlates with microsatellite instability (MSI), associated with tumor-infiltrating lymphocytes and programmed death ligand 1 (PD-L1) expression. This is the first case report in lung adenocarcinoma of ARID1A gene alterations leading to sporadic MSI, through somatic mutL homolog 1 (MLH1) promoter methylation, with an MLH1 gene mutation as the second somatic hit.

Case presentation
A 50-year-old never-smoker Bulgarian woman, with no comorbidities and no family history of cancer, was diagnosed with metastatic lung adenocarcinoma. PD-L1 immunohistochemistry (IHC) of tissue biopsies on right groin adenopathies resulted in 30% positivity. Liquid biopsy test reported actionable alterations in ARID1A gene, rearranged during transfection (RET) gene fusions, epidermal growth factor receptor (EGFR) gene R776H mutation, breast cancer (BRCA) genes 1/2, and cyclin-dependent kinase inhibitor 2A (CDKN2A) gene mutations. The patient was treated with immunotherapy, and showed a treatment response lasting for 19 months until a new metastasis appeared at the right deltoid muscle. Genomic analysis of a sample of this metastasis confirmed PD-L1 positivity of greater than 50% with CD8+ T cells expression and showed MSI with a deleterious c.298C>T (p.R100*) MLH1 gene mutation. Multiplex ligation-dependent probe amplification (MLPA) of this sample unveiled MLH1 gene promoter methylation. The MLH1 gene mutation and the MLH1 gene methylation were not present at the germline setting.

Conclusions
In this particular case, we show that ARID1A gene mutations with sporadic MSI due to somatic MLH1 gene promoter methylation and MLH1 gene mutation could change the prognosis and define the response to immunotherapy in a patient with lung adenocarcinoma. Comprehensive solid and liquid biopsy tests are useful to find out resistance mechanisms to immune checkpoint inhibitors. Our data encourages the development of new therapies against ARID1A mutations and epigenomic methylation when involved in MSI neoplasms.
Scabies-induced lichen simplex chronicus misdiagnosed as psychogenic pruritus: a case report
Authors: Emmanuel Ozzy M. , Karovska Ana V. , Ikedilo Okey 
Published: February 2021

Abstract
Introduction
Lichen simplex chronicus has been defined as a localized skin condition characterized by thickening, hyperpigmentation and accentuated skin markings from chronic itching and from repeated scratching. The affected skin area is usually described as demarcated, and often circumscribed. It has even been defined as a “psychogenic pruritic disorder”. The idea of a neurological component has also been suggested, hence the term 'neurodermatitis circumscripta'. However, the pathophysiology of this condition remains unclear. Several associations and etiologies have been reported in literature, including strong links with mental disorders—anxiety and obsessive compulsive disorder to be specific. We report this case, most importantly, to highlight the value of an open-minded approach to patients and the 'old-fashioned' physician character of empathy, the skill of detailed history taking and physical examination, and lastly to suggest that lichen simplex chronicus may not always present as a localized, 'circumscripta' or demarcated area of skin.

Case description
When a sixty-five year-old Caucasian female presented to our clinic agitated, intensely scratching her entire body and complaining of severe pruritus, an open-minded detailed approach during history taking and physical examination led to the working diagnosis of diffuse lichenification from chronic scratching secondary to a “possible” cutaneous disorder. Her medical history was unremarkable, but her psychiatric history was significant for Anxiety disorder. She remained on her anxiolytic medication. Her presenting symptom was reported to have persisted for more than 9 months. Review of previous unremarkable lab results and a remarkable findings on detailed skin inspection led to an empiric, trial regimen consisting of three topical preparations: an anti-pruritic—to break the itch-scratch cycle, anti-inflammatory—to curb any inflammatory/immune response and a 'last-ditch' scabicidal application. Follow-up was scheduled, but the patient called the office requesting an earlier follow up appointment. The lesions had significantly improved and the hyper-pigmented, indurated and escoriated skin appearance had resolved; and most importantly, the pruritus.

Conclusion
Thus we conclude that lichen simplex chronicus may not always present as circumscribed or localized area of skin as currently noted in literature. Also, in patients with psychiatric conditions including anxiety and obsessive-compulsive disorder in particular, effort should be made to avoid stereotyping their presentation as part of their mental disorder spectrum. The value of detailed history and physical examination, mixed with empathy is highlighted. We make our recommendation considering the profound turnaround in the patient's condition and quality of life after several months of emotional and psychological suffering.