Miracle-dz/UniFAR-FTUs huggingface dataset:
Global burden, risk factors, clinicopathological characteristics, molecular biomarkers and outcomes of microsatellite instability-high gastric cancer

Microsatellite instability-high (MSI-H) has gained considerable interests since it was approved as a tumor-agnostic biomarker in immunotherapy. However, the reported characteristics of MSI-H gastric cancer (GC) are inconsistent due to the biological complexity. Here, we aim to clarify the prevalence, risk factors, clinicopathological/molecular features and outcomes of MSI-H GC though a comprehensive review on 43246 patients from 134 cohorts. Overall, the proportion of MSI-H GC was 14.5% (95% CI, 13.3%-15.8%). Patients with MSI-H GC were less likely to have Epstein-Barr virus infection. High incidences of MSI-H GC were associated with female, older age, lower gastric body, Lauren intestinal histology, WHO tubular and mucinous subtypes, and early disease stage. Additionally, patients with MSI-H GC harbored more KRAS mutation, PD-L1 positivity, CD8 overexpression, and higher TMB, but less HER2 positivity and TP53 mutation. When treated with conventional strategy, the 5-year survival rates in MSI-H patients (70.3%) and MSI-L/MSS patients (43.7%) were significantly different (p<0.001). Patients with MSI-H GC derived larger benefit from immunotherapy in term of overall survival (pInteraction<0.001) and objective response (pInteraction=0.02). Since the prevalence of MSI-H GC is relatively high and associated with distinct clinicopathological and molecular characteristics, MSI testing should be conducted during standard diagnostical activity. Moreover, giving MSI-H tumors are often diagnosed at early stage and have favorable outcomes, less aggressive treatment strategies may be considered in clinical practice. In summary, this panoramic review may assist in design and/or interpretation of clinical trials, provide references in drug development, and constitute complementary information in drafting the clinical practice guideline.
Immune Escape Strategies in Head and Neck Cancer: Evade, Resist, Inhibit, Recruit

Simple Summary Head and neck cancer (HNC) is an aggressive form of cancer that affects hundreds of thousands of people worldwide and has a relatively poor prognosis. In the last decade, new therapeutics designed to enhance a patient’s immune system have been approved for use, but HNC has developed many different methods that help it escape the immune system. The existing immunotherapies target only one of these mechanisms, allowing HNC to utilize others to continue to elude the immune system. This review details the various strategies used by HNC to escape the immune response, dividing them into four general categories: evade, resist, inhibit, and recruit. Each of the immune escape mechanisms represents a potential immunotherapy target that could be used to treat HNC. Abstract Head and neck cancers (HNCs) arise from the mucosal lining of the aerodigestive tract and are often associated with alcohol use, tobacco use, and/or human papillomavirus (HPV) infection. Over 600,000 new cases of HNC are diagnosed each year, making it the sixth most common cancer worldwide. Historically, treatments have included surgery, radiation, and chemotherapy, and while these treatments are still the backbone of current therapy, several immunotherapies have recently been approved by the Food and Drug Administration (FDA) for use in HNC. The role of the immune system in tumorigenesis and cancer progression has been explored since the early 20th century, eventually coalescing into the current three-phase model of cancer immunoediting. During each of the three phases—elimination, equilibrium, and escape—cancer cells develop and utilize multiple strategies to either reach or remain in the final phase, escape, at which point the tumor is able to grow and metastasize with little to no detrimental interference from the immune system. In this review, we summarize the many strategies used by HNC to escape the immune system, which include ways to evade immune detection, resist immune cell attacks, inhibit immune cell functions, and recruit pro-tumor immune cells.
A Semantic-Based Scheduling Approach for Soft Real-Time Systems

In this paper a semantic classi(cid:28)cation of soft real-time tasks is introduced. The classi(cid:28)cation is done by the results that the tasks produce and it is used to propose a scheduling algorithm. The algorithm is called SIDS and it is based on the usage of server mechanisms. The priority of a server is managed accordingly to the result that its associated tasks produce. Along with the formal presentation of the algorithm and the proofs of its properties, a case study and some performance evaluations are included in the paper
Climate Variability & Rural Livelihoods The Vulnerability & Adaptation Strategy of Coastal zone Farming Community

The concept of social phenomenon encompasses the meaning of ‘Occasion’ rather than ‘event’. The idea social occasion draws analogy from analysis of many sociologists which implies that disasters provide multi-possibilities for human action for development rather than involving one liner path to an end result which implies an event. Sometimes these disasters best be seen as social crisis occasion (Quarantelli: 1986) . Human experiences of coping with disasters are best exemplified in the way the poor people cope with vulnerability. Though vulnerability is not the same as poverty but the poor people are more prone to vulnerability due to external shocks like disaster. Here we can say that climate is the primary important factor for agriculture based country as well as her famer’s socio –economic condition. But climate variability effect itself also varies within the same country. As a result, coastal area people are more vulnerable than the people live in highland. In Bangladesh poverty is the overriding issue which depicts the relationship between disasters and socio-economic factors. Its highlights social phenomenon and individual– collective behaviour in mitigating effects of disasters on poor. This study reviews the impacts of climate variability on agriculture sector. As a sociological study, the main interests are findings the socio-economic vulnerability of farmers along with the potential agricultural adaptation due to climate variability in Bangladesh. List of Abbreviations ADB Asian Development Bank ARAC Adaptation Research Advisory Committee BARC Bangladesh Agricultural Research Council BARI Bangladesh Agricultural Research Institute BRRI Bangladesh Rice Research Institute BUP Bangladesh Unnayan Parishad CEGIS Center for Environmental and Geographical Services CCC Climate Change Cell CDMP Comprehensive Disaster Management Program DAE Department of Agriculture Extension DoE Department of Environment DFID Department for International Development FAO Food and Agricultural Organization of the United Nations GCM General Circulation Models GDP Gross Domestic Products GoB Government of Bangladesh HYV High Yielding Variety IPCC Intergovernmental Panel on Climate Change MOEF Ministry of Environment and Forests NAPA National Adaptation Programme for Action RVCC Reducing Vulnerability to Climate Change SLR Sea Level Rise SRES Special Report on Emission Scenario STW Shallow Tube-Well TAR Third Assessment Report UK United Kingdom UNDP United Nations Development Program WB World Bank
Do the Differences in the Epiligament of the Proximal and Distal Parts of the Anterior Cruciate Ligament Explain Their Different Healing Capacities? Quantitative and Immunohistochemical Analysis of CD34 and α-SMA Expression in Relation to the Epiligament Theory

The aim of this study was to assess the epiligament theory by determining the normal epiligament morphology of the proximal and distal parts of the anterior cruciate ligament in humans and analyzing the differences between them and the midportion of the ligament in terms of cell numbers and expression of CD34 and α-SMA. Samples were obtained from the anterior cruciate ligaments of 12 fresh knee joints. Monoclonal antibodies against CD34 and α-SMA were used for immunohistochemistry. Photomicrographs were analyzed using ImageJ software, version 1.53f. The cell density was higher in the epiligament than in the ligament connective tissue. Cell counts were higher in the proximal and distal thirds than in the midsubstance of the epiligament. CD34 was expressed similarly in the proximal and distal thirds, although it seemed slightly more pronounced in the distal third. α-SMA expression was more robust in the proximal than the distal part. The results revealed that CD34 and α-SMA are expressed in the human epiligament. The differences between the numbers of cells in the proximal and distal parts of the epiligament and the expression of CD34 and α-SMA enhance epiligament theory. Future investigations into improving the quality of ligament healing should not overlook the epiligament theory.
rTMS reduces delta and increases theta oscillations in Alzheimer's disease: A visual‐evoked and event‐related potentials study

Abstract Background Repetitive transcranial magnetic stimulation (rTMS) has emerged as a promising alternative therapy for Alzheimer's disease (AD) due to its ability to modulate neural networks and enhance cognitive function. This treatment offers the unique advantage of enabling real‐time monitoring of immediate cognitive effects and dynamic brain changes through electroencephalography (EEG). Objective This study focused on exploring the effects of left parietal rTMS stimulation on visual‐evoked potentials (VEP) and visual event‐related potentials (VERP) in AD patients. Methods Sixteen AD patients were recruited for this longitudinal study. EEG data were collected within a Faraday cage both pre‐ and post‐rTMS to evaluate its impact on potentials. Results Significant alterations were found in both VEP and VERP oscillations. Specifically, delta power in VEP decreased, while theta power in VERP increased post‐rTMS, indicating a modulation of brain activities. Discussion These findings confirm the positive modulatory impact of rTMS on brain activities in AD, evidenced by improved cognitive scores. They align with previous studies highlighting the potential of rTMS in managing hyperexcitability and oscillatory disturbances in the AD cortex. Conclusion Cognitive improvements post‐rTMS endorse its potential as a promising neuromodulatory treatment for cognitive enhancement in AD, thereby providing critical insights into the neurophysiological anomalies in AD and possible therapeutic avenues.
Arctic Char, Salvelinus alpinus, Sport Fishery of Nalusiaq Lake, Auyuittuq National Park, Nunavut, May 2002 and 2004

Babaluk, J.A. , Ohokannoak, J., Schlosser, K. , Wastle, R.J., and Bajno, R. 2010. Arctic char, Salvelinus alpinus, sport fishery of Nalusiaq Lake, Auyuittuq National Park, Nunavut, May 2002 and 2004. Can. Manuscr. Rep. Fish. Aquat. Sci. 2933: ix + 69 p. During May 2002 and May 2004, creel censuses and biological surveys were conducted on the annual Arctic char, Salvelinus alpinus, sport fishing derby held on the Nalusiaq Lake system, Auyuittuq National Park, Nunavut. An estimated 425 fishers took part in the 2002 fishery while an estimated 427 fishers participated in 2004. Fishing pressure decreased from 2002 (1276 angling hours) to 2004 (673 angling hours). However, catch-per-unit-effort increased from 2002 (0.40 fish per hour) to 2004 (0.70 fish per hour). An estimated 510-515 Arctic char weighing a total of 822-830 kg were captured and retained in 2002 while in 2004, 472-474 Arctic char (822830 kg) were taken. The size range for the 2002 catch was 193-761 mm (fork length) with a mean length of 521 mm. In 2004, sizes ranged from 215-757 mm (mean = 546 mm). The age range for the 2002 catch was 6-21 years (mean = 12.6 years) while in 2004, ages ranged from 5-24 years (mean = 14.3 years). Two growth forms of Arctic char are present in Nalusiaq Lake: a fast-growing large form and slow-growing small form. Micro-chemical analysis of Arctic char otolith strontium distributions indicated an anadromous component to the population. Age-atfirst-migration to the sea ranged from 3+ years (fourth year of life) to 6+ years (seventh year of life).
Oral administration of resveratrol reduces oxidative stress generated in the hippocampus of Wistar rats in response to consumption of ethanol

Introduction Chronic ethanol intake has been found to favor hippocampal deterioration and alter neuronal morphological maturation; resveratrol has been suggested as an antioxidant that may counteract these effects. The objective of this study was to analyze the effect of resveratrol on oxidative stress markers, endogenous antioxidant system in the hippocampus, and the behavior of male Wistar rats administered different concentrations of ethanol. Methods The animals, at 3 months old, were randomly distributed into 11 study groups (n = 6/group), orally administered (5 days on, 2 days off) with water (control), ethanol (10, 20, 30, 40 or 50%), or ethanol (10, 20, 30, 40 or 50%) plus resveratrol (10 mg/Kg/day) for 2 months. Subsequently, the production of nitrites, malondialdehyde, and 4-hydroxy-alkenal (HNE) and the enzymatic activity of catalase and superoxide dismutase (SOD) were quantified. Results The levels of nitric oxide and lipid peroxidation products were significantly increased in each ethanol concentration and were statistically different compared to the control group; however, resveratrol significantly reduced oxidative stress caused by high ethanol concentration. The SOD and CAT did not present significant changes with respect to the controls in any of the study groups. In the different concentrations of ethanol used, GR increases significantly in the groups administered with resveratrol but not GPx. Resveratrol was shown to maintain the results similar to the control at most ethanol concentrations. Discussion Our results suggest that resveratrol prevents oxidative stress induced by ethanol in the hippocampus by decreasing cellular lipid peroxidation, but does not prevent the activation of catalase or SOD enzymes; however, allows glutathione to be kept active and in adequate concentrations in its reduced form and avoids alterations in the locomotor system.
Shear wave velocities in the upper mantle of the Western Alps: new constraints using array analysis of seismic surface waves

It remains challenging to obtain absolute shear wave velocities of heterogeneities of small lateral extension in the uppermost mantle. This study presents a cross-section of Vs across the strongly heterogeneous 3-D structure of the western European Alps, based on array analysis of data from 92 broad-band seismic stations from the CIFALPS experiment and from permanent networks in France and Italy. Half of the stations were located along a dense sublinear array. Using a combination of these stations and off-proﬁle stations, fundamental-mode Rayleigh wave dispersion curves were calculated using a combined frequency–time beamforming approach. We calculated dispersion curves for seven arrays of approximately 100 km aperture and 14 arrays of approximately 50 km aperture, the latter with the aim of obtaining a 2-D vertical cross-section of Vs beneath the western Alps. The dispersion curves were inverted for Vs ( z ), with crustal interfaces imposed from a previous receiver function study. The array approach proved feasible, as Vs ( z ) from independent arrays vary smoothly across the proﬁle length. Results from the seven large arrays show that the shear velocity of the upper mantle beneath the European plate is overall low compared to AK135 with the lowest velocities in the internal part of the western Alps, and higher velocities east of the Alps beneath the Po plain. The 2-D Vs model is coherent with (i) a ∼ 100 km thick eastward-dipping European lithosphere west of the Alps, (ii) very high velocities beneath the Po plain, coherent with the presence of the Alpine (European) slab and (iii) a narrow low-velocity anomaly beneath the core of the western Alps (from the Brianc¸onnais to the Dora Maira massif), and approximately colocated with a similar anomaly observed in a recent teleseismic P -wave tomography. This intriguing anomaly is also supported by traveltime variations of subvertically propagating body waves from two teleseismic events that are approximately located on the proﬁle great circle.
A new species of bristlebird (Passeriformes, Dasyornithidae) from the early Miocene of Australia

ABSTRACT The bristlebird family (Passeriformes, Dasyornithidae) constitutes one of the earliest branches in the oscine (songbird) tree. A new bristlebird, Dasyornis walterbolesi, sp. nov., is described from lower Miocene deposits of the Riversleigh World Heritage Area, Australia. This new species is based on a femur, a tibiotarsus, and a tarsometatarsus of one individual, the first known instance of associated passerine bones in the pre-Pleistocene record of Australia, as well as a distal part of a femur of a second individual. Dasyornis walterbolesi is smaller in size than the extant eastern bristlebird, D. brachypterus, and extends the known fossil record for Dasyornithidae by 18 million years. The new fossils considerably increase the geographic range of Dasyornithidae and indicate that the bristlebird family was once more widespread in Australia. A phylogenetic analysis of 91 morphological characters strongly supports the placement of the new fossil species in Dasyornithidae, although its intrafamilial relationships will only be better informed by discovery and study of additional material. Dasyornis walterbolesi meets five criteria for consideration as a well-justified fossil calibration and can be used to calibrate molecular estimates of the passerine evolutionary timescale.
Causal relationship between gut microbiota and kidney diseases: a two-sample Mendelian randomization study

Background The interplay between gut microbiome genera and inflammatory kidney-related diseases, such as nephrotic syndrome, glomerulonephritis, tubulo-interstitial nephritis, and chronic kidney disease, has been observed. However, the causal relationships between specific bacterial genera and these renal diseases have not been fully elucidated. Objective To investigate the potential causal links between different genera of the gut microbiome and the susceptibility to various renal conditions utilizing two-sample Mendelian randomization (MR) analyses. Materials and methods Genome-wide association study (GWAS) summary statistics of gut microbiota and inflammatory kidney-related diseases were obtained from published GWASs. Two-sample MR analyses were conducted using methods including inverse-variance weighted (IVW), MR Egger, and others to identify potential causal links between gut microbial genera and renal conditions. Sensitivity analyses, including Cochran’s Q test and the MR-PRESSO global test, were performed to validate the robustness of the results and detect horizontal pleiotropy. In addition, a reverse MR analysis was conducted to assess reverse causation possibilities. Results By synthesizing insights from both primary and sensitivity analyses, this study unveiled critical associations of 12 bacterial genera with nephrotic syndrome, 7 bacterial genera with membranous nephropathy, 3 bacterial genera with glomerulonephritis, 4 bacterial genera with acute tubulo-interstitial nephritis, 6 bacterial genera with chronic tubulo-interstitial nephritis, and 7 bacterial genera with chronic kidney disease. Various genera were pinpointed as having either positive or negative causal relationships with these renal conditions, as evidenced by specific ranges of IVW-OR values (all P< 0.05). The congruence of the sensitivity analyses bolstered the primary findings, displaying no marked heterogeneity or horizontal pleiotropy. Notably, the reverse MR analysis with nephritis as the exposure did not reveal any causal relationships, thereby strengthening the resilience and validity of the primary associations. Conclusion This study explored the causal associations between several gut microbial genera and the risk of several inflammatory kidney-related diseases, uncovering several associations between specific gut microbial genera and nephrotic syndrome, membranous nephropathy, glomerulonephritis, tubulo-interstitial nephritis, and chronic kidney disease. These findings enhance our understanding of the complex interplay between the gut microbiome and kidney diseases, and they will be beneficial for early diagnosis and subsequent treatment.
Association of non-contrast CT markers with long-term functional outcome in deep intracerebral hemorrhage

Objective Hematoma expansion (HE) is the most important therapeutic target during acute care of patients with intracerebral hemorrhage (ICH). Imaging biomarkers such as non-contrast CT (NCCT) markers have been associated with increasing risk for HE. The aim of the present study was to evaluate the influence of NCCT markers with functional long-term outcome and with HE in patients with deep (basal ganglia and thalamus) ICH who represent an important subgroup of patients at the highest risk for functional deterioration with HE due to the eloquence of the affected brain region. Methods From our prospective institutional database, all patients maximally treated with deep ICH were included and retrospectively analyzed. NCCT markers were recorded at diagnostic imaging, ICH volume characteristics were volumetrically evaluated, and all patients received follow-up imaging within 0–48 h. We explored associations of NCCT makers with unfavorable functional outcome, defined as modified Rankin scale 4–6, after 12 months and with HE. Bias and confounding were addressed by multivariable regression modeling. Results In 322 patients with deep ICH, NCCT markers were distributed as follows: irregular shape: 69.6%, heterogenous density: 55.9%, hypodensities: 52.5%, island sign: 19.3%, black hole sign: 11.5%, and blend sign: 4.7%. Upon multivariable regression analyses, independent associations were documented with the functional outcome for irregular shape (aOR: 2.73, 95%CI: 1.42–5.22, p = 0.002), heterogenous density (aOR: 2.62, 95%CI: 1.40–4.90, p = 0.003) and island sign (aOR: 2.54, 95%CI: 1.05–6.14, p = 0.038), and with HE for heterogenous density (aOR: 5.01, 95%CI: 1.93–13.05, p = 0.001) and hypodensities (aOR: 3.75, 95%CI: 1.63–8.62, p = 0.002). Conclusion NCCT markers are frequent in deep ICH patients and provide important clinical implications. Specifically, markers defined by diverging intra-hematomal densities provided associations with a 5-times higher risk for HE and a 2.5-times higher likelihood for unfavorable functional long-term outcome. Hence, these markers allow the identification of patients with deep ICH at high risk for clinical deterioration due to HE.
Creation and Validation of an Automated Registry for Outpatient Parenteral Antibiotics

Abstract Existing outpatient parenteral antibiotic therapy (OPAT) registries are resource intensive, and OPAT programs struggle to produce objective data to show the value of their work. We describe the building and validation of an automated OPAT registry within our electronic medical record and provide objective data on the value of the program. Variables and outcomes include age, sex, race, ethnicity, primary insurance payor, antibiotic names, infection syndromes treated, discharge disposition, 30-day all-cause readmission and death rates, complications, and an estimate of the hospital days saved. Records for 146 OPAT episodes were reviewed manually to validate the registry. Data were displayed in a dashboard within the electronic medical record. Over the 4-year time frame, our registry collected 3956 unique patients who completed 4710 episodes (approximately 1200 episodes per year). A total of 400 complications during OPAT were identified. All variables had an accuracy of >90% on validation. The OPAT program resulted in a reduction in hospital length of stay by 88 820 days, or roughly 22 000 days per year. We intend our registry to serve as a blueprint for similar OPAT programs with limited administrative resources. Wider application of our system would allow for easier aggregation and comparisons of OPAT practice and address the lack interinstitutional standardization of OPAT data and outcomes.