Miracle-dz/UniFAR-FTUs huggingface dataset:
Geriatric Nutritional Risk Index as a Screening Tool to Identify Patients with Malnutrition at a High Risk of In-Hospital Mortality among Elderly Patients with Femoral Fractures—A Retrospective Study in a Level I Trauma Center

Background: Malnutrition is frequently underdiagnosed in geriatric patients and is considered to be a contributing factor for worse outcomes during hospitalization. In addition, elderly patients who undergo trauma are often malnourished at the time of incurring fractures. The geriatric nutritional risk index (GNRI), calculated based on the serum albumin level and the ratio of present body weight to ideal body weight, was proposed for the assessment of the nutritional status of elderly patients with various illnesses. This study aimed to investigate whether the GNRI has a prognostic value that links the nutritional status and mortality outcomes of elderly patients who have previously undergone trauma with femoral fractures. Methods: From January 1, 2009 to December 31, 2019, a total of 678 elderly patients with femoral fractures were categorized into four nutritional risk groups: a major-risk group (GNRI < 82; group 1, n = 127), moderate-risk group (GNRI 82–92; group 2, n = 179), low-risk group (GNRI 92–98; group 3, n = 123), and no-risk group (GNRI > 98; group 4, n = 249). To minimize the confounding effects of sex, age, preexisting comorbidities, and injury severity of patients on outcome measurements, propensity score-matched patient cohorts were created to assess the impact of patients being in different nutritional risk groups on the in-hospital mortality outcomes against the no-risk group. Results: The patients in groups 1–3 were significantly older and presented a significantly lower body mass index and lower serum albumin levels than those in group 4. Compared with patients in group 4 (3.6%), a significantly higher mortality rate was found in the patients in group 1 (17.3%, p < 0.001), but not in those in group 2 (6.7%) or group 3 (2.4%). The study of propensity score-matched patient cohorts provided similar results; group 1 patients had significantly higher odds of mortality than group 4 patients (odds ratio, 6.3; 95% confidence interval, 1.34–29.37; p = 0.009), but there were no significant differences in mortality risks among patients in groups 2 and 3 compared with those in group 4. Conclusions: This preliminary study suggested that the GNRI may be used as a screening tool to identify patients with malnutrition at a high risk of mortality among elderly patients with femoral fractures. A prospective study is needed to validate the suggestion.
Distribution and bio-ecological features of Posidonia oceanica meadows along the coasts of the southern Adriatic and northern Ionian Seas

An update of the spatial distribution and bio-ecological features of Posidonia oceanica (L.) Delile meadows spread along the coasts of the southern Adriatic and northern Ionian Seas (Apulia region, southern Italy) is reported. Mapping carried out in 2004 indicated a remarkable reduction in the spatial distribution of P. oceanica meadows in the southern Adriatic Sea, mostly northwards of Bari, when compared with 1991 data. By contrast, in the northern Ionian Sea, the spatial distribution seems to be more stable. The P. oceanica meadows covered ∼330 km2 distributed along a total of 320 linear km coastline, mostly on the southern side of Apulia. Within natural variability, the differences in bio-ecological features could be due mainly to the presence of anthropic disturbance (urban, industrial and tourist pressure) rather than a significant geographical gradient between the Adriatic and Ionian Seas. However, the mean density values recorded in almost all the Adriatic stations fall within the ‘lower sub-normal density’ (LSD) range. By contrast, the mean density values observed in the Ionian meadows were generally within the ‘normal density’ (ND) range.
A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database

SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variant data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.
Interventional stroke treatment – Is it also safe for arteries? Looking at thrombectomy wall damage through clot histology

Background and purpose The aim of this study was to investigate whether morphological evidence of intracranial vascular injury can be found in the occluding thrombi of patients with ischemic stroke. Methods From 2015 until 2018 specimens of thrombi from patients with large vessel occlusion treated either by stent-assisted aspiration thrombectomy (TE) or by aspiration thrombectomy were prospectively collected. Thrombus specimens were formalin-fixed, paraffin-embedded and stained. Architectural features, presence of parts of vessel wall or atheromatous material, organisation of the thrombi, technique and number of thrombectomy manoeuvers were evaluated. Results Thrombus specimens from 302 patients were analyzed. 238 (80%) patients were treated with stent-assisted aspiration TE and 64 (20%) patients with aspiration TE only. 286 (95%) had fresh thrombi, 14 (4.6%) showed initial/complete thrombus organisation and multi-staged thrombi were found in 2 (<1%) patients. In 8 patients (2.6%) we found atypical thrombus content after a time interval longer 6 hours after onset and final thrombectomy manoeuvre: 4 with atheromatous material and 4 with parts of a vessel wall. In 1 patient with parts of vessel wall angiographically a dissection was detected. No parts of the vessel wall were found after sole aspiration thrombectomy. Conclusions The overall risk of arterial vessel wall injury aspiration thrombectomy was low in our study. Aspiration thrombectomy and the procedure related with a retrieving device together with an ischemia time longer than 6 hours may increase the risk of vessel injury through the thrombectomy procedure. Further investigations are necessary to elucidate the influence of the mentioned aspects.
A Comprehensive Study about the Role of Crosslink Density on the Tribological Behavior of DLC Coated Rubber

The friction and wear behavior of coated rubber components is strongly dependent on the substrate properties. This work deals with the impact of the crosslink density, i.e., the hardness of the rubber substrate on the tribological performance of uncoated and coated rubber. The hardness of nitrile butadiene rubber (NBR) is varied altering the sulfur content. Both the uncoated and coated rubber samples are characterized in terms of surface and mechanical properties. Tribological tests comprise the examination of the macroscopic contact area and the temperature in the contact zone. It was found that the functional layer enhances the wear resistance significantly. Apparently, the wear and friction behavior of the coated rubber correlates with the hardness and the bulk properties of the substrate material.
Hybrid closed‐loop therapy: Where are we in 2021?

Hybrid closed‐loop systems are characterized by the coexistence of algorithm‐driven automated insulin delivery combined with manual mealtime boluses. Used correctly, these insulin delivery systems offer better glucose control and reduced risk of hypoglycaemia and represent the most advanced form of insulin delivery available for people with type 1 diabetes. The aim of this paper was to compare the currently available commercial hybrid closed‐loop systems in the UK: the Medtronic 670G/780G, Tandem t:slim X2 Control IQ and CamAPS FX systems. The Medtronic 670G/780G systems use Guardian 3 sensor (7‐day use, two to four calibrations per day), while Tandem and CamAPS systems use the calibration‐free Dexcom G6 sensor (10 days). The CamAPS system is available as an android app, whereas the other two systems have the algorithm embedded in the insulin pump. During pivotal studies, depending on the study population and baseline glycated haemoglobin level, these systems achieve a time spent in the target range 3.9 to 10 mmol/L (70 to 180 mg/dL) of 65% to 76% with low burden of hypoglycaemia. All three systems allow a higher glucose target for announced exercise, while the Tandem system offers an additional night‐time tighter target. The CamAPS system offers fully customizable glucose targets and is the only system licensed for use during pregnancy. Additional education is required for both users and healthcare professionals to harness the best performance from these systems as well as to troubleshoot when “automode exits” occur. We provide consensus recommendations to develop pragmatic pathways to guide patients, clinicians and commissioners in making informed decisions on the appropriate use of the diabetes technology.
CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Abstract Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.
Comparative Analytical Evaluation of Four Centralized Platforms for the Detection of Mycobacterium tuberculosis Complex and Resistance to Rifampicin and Isoniazid

Failure to rapidly identify drug-resistant tuberculosis (TB) increases the risk of patient mismanagement, the amplification of drug resistance, and ongoing transmission. We generated comparative analytical data for four automated assays for the detection of TB and multidrug-resistant TB (MDR-TB): Abbott RealTime MTB and MTB RIF/INH (Abbott), Hain Lifescience FluoroType MTBDR (Hain), BD Max MDR-TB (BD), and Roche cobas MTB and MTB-RIF/INH (Roche). ABSTRACT Failure to rapidly identify drug-resistant tuberculosis (TB) increases the risk of patient mismanagement, the amplification of drug resistance, and ongoing transmission. We generated comparative analytical data for four automated assays for the detection of TB and multidrug-resistant TB (MDR-TB): Abbott RealTime MTB and MTB RIF/INH (Abbott), Hain Lifescience FluoroType MTBDR (Hain), BD Max MDR-TB (BD), and Roche cobas MTB and MTB-RIF/INH (Roche). We included Xpert MTB/RIF (Xpert) and GenoType MTBDRplus as comparators for TB and drug resistance detection, respectively. We assessed analytical sensitivity for the detection of the Mycobacterium tuberculosis complex using inactivated strains (M. tuberculosis H37Rv and M. bovis) spiked into TB-negative sputa and computed the 95% limits of detection (LOD95). We assessed the accuracy of rifampicin and isoniazid resistance detection using well-characterized M. tuberculosis strains with high-confidence mutations accounting for >85% of first-line resistance mechanisms globally. For H37Rv and M. bovis, we measured LOD95 values of 3,781 and 2,926 (Xpert), 322 and 2,182 (Abbott), 826 and 4,301 (BD), 10,398 and 23,139 (Hain), and 2,416 and 2,136 (Roche) genomes/ml, respectively. Assays targeting multicopy genes or targets (Abbott, BD, and Roche) showed increased analytical sensitivity compared to Xpert. Quantification of the panel by quantitative real-time PCR prevents the determination of absolute values, and results reported here can be interpreted for comparison purposes only. All assays showed accuracy comparable to that of Genotype MTBDRplus for the detection of rifampicin and isoniazid resistance. The data from this analytical study suggest that the assays may have clinical performances similar to those of WHO-recommended molecular TB and MDR-TB assays.
Interstitial telomere sequences disrupt break-induced replication and drive formation of ectopic telomeres

Abstract Break-induced replication (BIR) is a mechanism used to heal one-ended DNA double-strand breaks, such as those formed at collapsed replication forks or eroded telomeres. Instead of utilizing a canonical replication fork, BIR is driven by a migrating D-loop and is associated with a high frequency of mutagenesis. Here we show that when BIR encounters an interstitial telomere sequence (ITS), the machinery frequently terminates, resulting in the formation of an ectopic telomere. The primary mechanism to convert the ITS to a functional telomere is by telomerase-catalyzed addition of telomeric repeats with homology-directed repair serving as a back-up mechanism. Termination of BIR and creation of an ectopic telomere is promoted by Mph1/FANCM helicase, which has the capacity to disassemble D-loops. Other sequences that have the potential to seed new telomeres but lack the unique features of a natural telomere sequence, do not terminate BIR at a significant frequency in wild-type cells. However, these sequences can form ectopic telomeres if BIR is made less processive. Our results support a model in which features of the ITS itself, such as the propensity to form secondary structures and telomeric protein binding, pose a challenge to BIR and increase the vulnerability of the D-loop to dissociation by helicases, thereby promoting ectopic telomere formation.
Information ecology ‐ a viewpoint

Information ecology is a science which studies the laws governing the influence of information summary on the formation and functioning of bio‐systems, including that of individuals, human communities and humanity in general and on the health and psychological, physical and social well‐being of the human being; and which undertakes to develop methodologies to improve the information environment. The paper outlines suggested areas of studies.
ASC-Mediated Inflammation and Pyroptosis Attenuates Brucella abortus Pathogenesis Following the Recognition of gDNA

Brucella abortus is a zoonotic pathogen that causes brucellosis. Because of Brucella’s unique LPS layer and intracellular localization predominately within macrophages, it can often evade immune detection. However, pattern recognition receptors are capable of sensing Brucella pathogen-associated molecular patterns (PAMPS). For example, NOD-like receptors (NLRs) can form a multi-protein inflammasome complex to attenuate Brucella pathogenesis. The inflammasome activates IL-1β and IL-18 to drive immune cell recruitment. Alternatively, inflammasome activation also initiates inflammatory cell death, termed pyroptosis, which augments bacteria clearance. In this report, we assess canonical and non-canonical inflammasome activation following B. abortus infection. We conducted in vivo studies using Asc−/− mice and observed decreased mouse survival, immune cell recruitment, and increased bacteria load. We also conducted studies with Caspase-11−/− mice and did not observe any significant impact on B. abortus pathogenesis. Through mechanistic studies using Asc−/− macrophages, our data suggests that the protective role of ASC may result from the induction of pyroptosis through a gasdermin D-dependent mechanism in macrophages. Additionally, we show that the recognition of Brucella is facilitated by sensing the PAMP gDNA rather than the less immunogenic LPS. Together, these results refine our understanding of the role that inflammasome activation and pyroptosis plays during brucellosis.
Clinical Evaluation of Time Efficiency and Fit Accuracy of Lithium Disilicate Single Crowns between Conventional and Digital Impression

The purpose of this study was to demonstrate the time-efficiency and the clinical effectiveness of chairside-fabricated lithium disilicate single crowns by digital impressions compared to the conventional method. Thirteen patients requiring a single crown on the maxillary or mandibular premolar or first molar were assigned as study subjects. The impressions were obtained using the conventional method and two digital methods with intraoral scanners: AEGIS.PO (Digital Dentistry Solution, Seoul, Korea) and CEREC Omnicam (Sirona, Bensheim, Germany). Two types of lithium disilicate single crowns were obtained; a reference crown (by conventional workflow) and a chairside crown (by digital workflow). The total time taken for fabricating the chairside crown was recorded. The replica technique was performed to compare the marginal and internal fit of the two types of crowns. In addition, accuracy of the intraoral scanners was evaluated by the best-fit alignment method. The difference between the groups was analyzed using the two-tailed paired t-test or one-way ANOVA, followed by the Student–Newman–Keuls test for multiple comparisons. Statistical significance was accepted at p < 0.05 for all statistical tests. The time required to obtain the impressions by the AEGIS (7:16 ± 1:50 min:s) and CEREC (7:29 ± 2:03 min:s) intraoral scans was significantly lower than the conventional method (12:41 ± 1:16 min:s; p < 0.001). There was no significant difference between the intraoral scanners. The total working time to fabricate the chairside crown averaged 30:58 ± 4:40 min:s. The average marginal gap was not significantly different between the reference (107.86 ± 42.45 µm) and chairside (115.52 ± 38.22 µm) crowns (p > 0.05), based on results of replica measurement. The average internal gaps were not significantly different. The average value of the root mean square between the AEGIS (31.7 ± 12.3 µm) and CEREC (32.4 ± 9.7 µm) scans was not significantly different (p > 0.05). Intraoral scans required a significantly shorter impression time than the conventional method, and it was possible to fabricate a lithium disilicate crown in a single visit. There were no statistically significant differences in the fit of the restorations and accuracy of the intraoral scanners compared to the conventional workflow.
Oncogenic Roles of RAD51AP1 in Tumor Tissues Related to Overall Survival and Disease-Free Survival in Hepatocellular Carcinoma

Objective: This study aimed to investigate the associations between RAD51AP1 and the outcomes of hepatocellular carcinoma (HCC). Methods: RAD51AP1 expression levels were compared in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets. The Liver Hepatocellular Carcinoma (TCGA, Provisional) and GSE36376 datasets were used for survival analysis. RAD51AP1 associations with clinicopathological features were determined with the GSE36376 dataset. Results: RAD51AP1 mRNA expression was significantly upregulated in advanced liver fibrosis samples (S3-4 vs. S0-2 and G3-4 vs. G0-2) from hepatitis B virus (HBV)-related liver fibrosis patients and in tumor tissues and peripheral blood mononuclear cells (PBMCs) from HCC patients (all P < 0.05). HCC patients with high RAD51AP1 expression had significantly worse overall survival (OS) and disease-free survival (DFS) than those with low RAD51AP1 expression (P = 0.0034 and P = 0.0012, respectively) in the TCGA dataset, and these findings were validated with the GSE36376 dataset (P = 0.0074 and P = 0.0003, respectively). A Cox regression model indicated that RAD51AP1 was a risk factor for OS and DFS in HCC patients in GSE36376 (HR = 1.54, 95% CI = 1.02-2.32, P = 0.04 and HR = 1.71, 95% CI = 1.22-2.39, P = 0.002, respectively). Moreover, RAD51AP1 mRNA expression increased gradually with increasing tumor stage, including stratification by American Joint Committee on Cancer (AJCC) stages, Barcelona Clinic Liver Cancer (BCLC) stages and Edmondson grades. In addition, RAD51AP1 was overexpressed in HCC patients with intrahepatic metastasis, major portal vein invasion, vascular invasion and/or an alpha-fetoprotein (AFP) level > 300 ng/ml. Conclusions: Contributing to an advanced tumor stage, intrahepatic metastasis, vascular invasion and AFP level elevation, RAD51AP1 upregulation was significantly associated with OS and DFS in HCC patients.
Citrullination-Resistant LL-37 Is a Potent Antimicrobial Agent in the Inflammatory Environment High in Arginine Deiminase Activity

LL-37, the only member of the mammalian cathelicidin in humans, plays an essential role in innate immunity by killing pathogens and regulating the inflammatory response. However, at an inflammatory focus, arginine residues in LL-37 can be converted to citrulline via a reaction catalyzed by peptidyl-arginine deiminases (PAD2 and PAD4), which are expressed in neutrophils and are highly active during the formation of neutrophil extracellular traps (NETs). Citrullination impairs the bactericidal activity of LL-37 and abrogates its immunomodulatory functions. Therefore, we hypothesized that citrullination-resistant LL-37 variants would retain the functionality of the native peptide in the presence of PADs. To test this hypothesis, we synthetized LL-37 in which arginine residues were substituted by homoarginine (hArg-LL-37). Bactericidal activity of hArg-LL-37 was comparable with that of native LL-37, but neither treatment with PAD4 nor exposure to NETs affected the antibacterial and immunomodulatory activities of hArg-LL-37. Importantly, the susceptibilities of LL-37 and hArg-LL-37 to degradation by proteases did not significantly differ. Collectively, we demonstrated that citrullination-resistant hArg-LL-37 is an attractive lead compound for the generation of new agents to treat bacterial infections and other inflammatory diseases associated with enhanced PAD activity. Moreover, our results provide a proof-of-concept for synthesis of therapeutic peptides using homoarginine.