Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy in Traumatic Brain Injury: A New Target for Therapeutic Intervention

Traumatic brain injury (TBI) is one of the most devastating forms of brain injury. Many pathological mechanisms such as oxidative stress, apoptosis and inflammation all contribute to the secondary brain damage and poor outcomes of TBI. Current therapies are often ineffective and poorly tolerated, which drive the explore of new therapeutic targets for TBI. Autophagy is a highly conserved intracellular mechanism during evolution. It plays an important role in elimination abnormal intracellular proteins or organelles to maintain cell stability. Besides, autophagy has been researched in various models including TBI. Previous studies have deciphered that regulation of autophagy by different molecules and pathways could exhibit anti-oxidative stress, anti-apoptosis and anti-inflammation effects in TBI. Hence, autophagy is a promising target for further therapeutic development in TBI. The present review provides an overview of current knowledge about the mechanism of autophagy, the frequently used methods to monitor autophagy, the functions of autophagy in TBI as well as its potential molecular mechanisms based on the pharmacological regulation of autophagy.
Can inflammatory markers in induced sputum be used to detect phenotypes and endotypes of pediatric severe therapy‐resistant asthma?

The phenotypes and endotypes of severe therapy‐resistant asthma (STRA) have not been fully elucidated in children. The aim of the present study was to investigate inflammatory markers in the induced sputum of children with STRA and to compare them with those present in a group of children who achieved control.
Examination of the effect of ovarian radiation injury induced by hysterosalpingography on ovarian proliferating cell nuclear antigen and the radioprotective effect of amifostine: an experimental study

Aim The aim of this study was to examine the effect of amifostine on cellular injury in the ovarian tissue induced by hysterosalpingography (HSG). Methods In total, forty 4-month old female Wistar Albino rats were assigned into 8 groups. Each group contained 5 rats. Group 1 (G1): rats were decapitated without any procedure. Group 2 (G2): rats were decapitated after 3 hours of total body irradiation. Group 3 (G3): rats were decapitated 3 hours after HSG procedure. Group 4 (G4): rats were decapitated 3 hours after HSG procedure performed 30 min after receiving amifostine 200 mg/kg intraperitoneally. Group 5 (G5): rats were decapitated after 1 month without any procedure. Group 6 (G6): rats were decapitated after 1 month of total body irradiation. Group 7 (G7): rats were decapitated 1 month after HSG procedure. Group 8 (G8): rats were decapitated 1 month after HSG procedure performed 30 min after receiving amifostine 200 mg/kg intraperitoneally. After rats were decapitated under general anesthesia in all groups, blood samples were obtained and bilateral ovaries were removed. One of the ovaries was placed in 10% formaldehyde solution for histological germinal epithelial degeneration, apoptosis and proliferating cell nuclear antigen scoring. The other ovary and blood sera were stored at −80°C. TNF-α, total antioxidant status, total oxidant status, and malondialdehyde levels were studied in tissue samples and anti-mullerian hormone levels in blood samples. Results At the end of the first month, there was significant ovarian germinal epithelium degeneration. Proliferating cell nuclear antigen immunoreactivity was significantly reduced in all other groups when compared with G1 and G5. Conclusion In conclusion, amifostine could significantly reduce the ovarian cellular injury induced by HSG.
Data flow metrics in program comprehension tasks

Existing research in program comprehension has paid less attention to the coverage of programming concepts that were contained within the source codes used for studies. In this paper, we examine source codes covering four introductory programming concepts: branching, loops and arrays, sorting, and tail recursion. The diverse types of code fragments give rise to eye movement patterns more structured according to the control flow and data flow of the program. To facilitate analysis of this class of program comprehension strategies, we propose data flow-based metrics and describe automatic computation of the metrics. In evaluation of the proposal, we conducted a pilot study with novice and intermediate programmers. In the study with recordings from 26 programmers we compute basic fixation and saccade metrics along with a data flow-based metric.
From Latency, Through Outbreak, to Decline: Detecting Different States of Emergency Events Using Web Resources

An emergency event is a sudden, urgent, usually unexpected incident or occurrence that requires an immediate reaction or assistance for emergency situations, which plays an increasingly important role in the global economy and in our daily lives. Recently, the web is becoming an important event information provider and repository due to its real-time, open, and dynamic features. In this paper, web resources based states detecting algorithm of an event is developed in order to let the people know of an emergency event clearly and help the social group or government process the emergency events effectively. The relationship between web and emergency events is first introduced, which is the foundation of using web resources to detect the state of emergency events imaged on the web. Second, five temporal features of emergency events are developed to provide the basis for state detection. Moreover, the outbreak power and the fluctuation power are presented to integrate the above temporal features for measuring the different states of an emergency event. Using these two powers, an automatic state detecting algorithm for emergency events is proposed. In addition, heuristic rules for detecting the states of emergency event on the web are discussed. Our evaluations using real-world data sets demonstrate the utility of the proposed algorithm, in terms of performance and effectiveness in the analysis of emergency events.
Models including serum CA-125, BMI, cyst pathology, dysmenorrhea or dyspareunia for diagnosis of endometriosis.

AIM To evaluate preoperative levels of CA-125 and HE4 in patients with endometriosis-like symptoms and to construct diagnostic models. PATIENTS Prospective case-control study included 124 endometriosis patients and 97 control patients. MATERIALS & METHODS Logistic regression was used to construct diagnostic models based on serum biomarker levels and clinical data. RESULTS A model with CA-125, BMI, information on cysts and dyspareunia had an area under the curve value of 0.836, sensitivity of 74.0% and specificity of 81.3%. The second model included CA-125, BMI, information on cysts and dysmenorrhea and had an area under the curve value of 0.819, sensitivity of 74.8% and specificity of 79.2%. CONCLUSION Constructed models have the potential for noninvasive diagnosis of endometriosis, and might be translated into clinical practice after additional validation.
Efficient Parameter Estimation for Information Retrieval Using Black-Box Optimization

The retrieval function is one of the most important components of an Information Retrieval (IR) system, because it determines to what extent some information is relevant to a user query. Most retrieval functions have “free parameters” whose value must be set before retrieval, significantly affecting the effectiveness of an IR system. Choosing the optimum values for such parameters is therefore of paramount importance. However, the optimum can only be found after a computationally expensive process, especially when the generalization error is estimated via cross-validation. In this paper, we propose to determine free parameter values by solving an optimization problem aimed at maximizing a measure of retrieval effectiveness. We employ the black-box optimization paradigm, since the analytical expression of the measure of effectiveness with respect to the free parameters is unknown. We consider different methods for solving the black-box optimization problem: a simple grid-search over the whole domain, and more sophisticated techniques such as line search and surrogate model based algorithms. Experimental results on several test collections not only provide useful insight about effectiveness, but also about efficiency: they indicate that with appropriate optimization techniques, the computational cost of parameter optimization can be greatly reduced without compromising retrieval effectiveness, even when taking generalization into account.
Osteonecrosis of the femoral head in people living with HIV: anatomopathological description and p24 antigen test

Objective To examine the presence of HIV in bone tissue of people living with HIV (PLWHIV) with osteonecrosis of femoral head and describe clinical and anatomopathological findings. Design This is a case series which included 44 PLWHIV with osteonecrosis of femoral head who underwent total hip arthroplasty. Methods Clinical data were obtained through analysis of the patients’ medical records. Bone tissue obtained during total hip arthroplasty was retrieved and sent for conventional and immunohistochemical analysis. Monoclonal antibodies were used to mark the p24 (HIV), CD31 (vascular endothelial cells), CD68 (macrophages), and D240 (cells of the lymphatic endothelium) antigens. Results Dyslipidemia was found in 48% of the patients and lipodystrophy in 31%. Histological analysis showed similar characteristics for the entire sample. Degeneration of joint cartilage was visualized with the presence of fissures and fibrillations, as well as subchondral sclerosis and necrosis of the subchondral cancellous bone tissue. Lymphoplasmocytic inflammatory reaction was observed, with the presence of macrophages containing a foamy, vacuolated cytoplasm, as well as the presence of ceroid pigment and occasional granulation tissue. The reaction with the monoclonal anti-p24 antibody was negative in the samples from all 44 PLWHIV undergoing hip arthroplasty. Reactions with the anti-CD31 and anti-D240 antibodies were negative. Staining with CD68 antibody confirmed that the cells visualized with foamy, vacuolated cytoplasm were macrophages. Conclusion p24 HIV antigen was not detected in the bone tissue of PLWHIV and osteonecrosis. The most frequent anatomopathological findings were extensive necrosis of bone tissue, large vacuoles filled with fat cells, inflammatory lymphoplasmocytic reaction with macrophages containing vacuolated cytoplasm, and the presence of ceroid pigment.
An approach to power assist hand exoskeleton for patients with paralysis

The aim of this paper is to propose a novel robotic hand exoskeleton which can assist disabled people with grasping objects. Existing exoskeletons cannot measure force during contact motion, and this makes it difficult to achieve accurate grasp assistance. In the proposed system the exoskeletal finger is attached to the index and middle fingers, and the robotic finger is place on the palm side, which functions as a substitute of a thumb. The upper exoskeletal finger exerts assistive force on operator's fingers, and the lower robotic finger works as a force sensor by the use of Reaction Torque Observer. Thus, human grasping force is measured during grasping, and the environmental and human forces are estimated from measured torque. The proposed system realizes power assist control without using additive sensors like force sensors or EMG sensors. The effectiveness of the proposed method is demonstrated through simulation and experiment.
TOBTD: Throughput debugging in total-order broadcast systems

Systems running Total-Order Broadcast protocols are prone to throughput downgrades due to both system-level failures (anomalies and crashes) and network level failures (background traffic and byzantine failures). Such systems require persistent throughput debugging notably in multi-datacenter environments, that are characterized by non-uniform network connectivity. This paper presents a novel algorithm that debugs throughput of Total-Order Broadcast primitives automatically in the multi-datacenter environments. More precisely, it is a configuration methodology for improving the throughput of a black-box system in the presence of background traffic.
Studies of the Reactivity of the Ferrihydrite Surface by Iron Isotopic Exchange and Mössbauer Spectroscopy

Two-line ferrihydrite is an important adsorbent of many toxics in natural and anthropogenic systems; however, the specific structural sites responsible for the high adsorption capacity are not well understood. A combination of chemical and spectroscopic techniques have been employed in this study to gain further insight into the structural nature of sites at the ferrihydrite surface. The kinetics of iron isotopic exchange demonstrated that there are at least two types of iron sites in ferrihydrite. One population of sites, referred to as labile sites, approached iron isotopic equilibrium within 24 hr in 59Fe-NTA solutions, while the second population of sites, referred to as non-labile, exhibited a much slower rate of isotopic exchange. Adsorbed arsenate reduced the degree of exchange by labile sites, indicating that the anion blocked or greatly inhibited the rate of exchange of these sites. Mössbauer spectra were collected from a variety of samples including 56Fe-ferrihydrite samples with 57Fe in labile sites, samples containing 57Fe throughout the structure, and samples with 57Fe in non-labile sites. The spectra showed characteristic broad doublets signifying poor structural order. Refined fits of the spectra indicated that labile sites have larger quadrupole splitting, hence more local distortion, than non-labile sites. In all cases, the spectra demonstrated some degree of asymmetry, indicating a distribution of Fe environments in ferrihydrite. Overall spectral findings, combined with recent EXAFS results (Waychunas et al., 1993), indicate that labile sites likely are more reactive (with respect to iron isotopic exchange) because they have fewer neighboring Fe octahedra and are therefore bound less strongly to the ferrihydrite structure. The labile population of sites probably is composed of end sites of the dioctahedral chain structure of 2-line ferrihydrite, which is a subset of the entire population of surface sites. Mössbauer spectra of samples containing adsorbed arsenate indicated that the anion may slightly decrease the distortion of labile sites and stabilized the structure as a whole by bidentate bonding.
Comparison of carboplatin plus etoposide with amrubicin monotherapy for extensive‐disease small cell lung cancer in the elderly and patients with poor performance status

Carboplatin plus etoposide (CE) is a standard treatment for elderly patients with extensive‐disease small cell lung cancer (ED‐SCLC). However, amrubicin monotherapy (AMR) may be a feasible alternative. We compared the efficacies and safety profiles of CE and AMR for ED‐SCLC in elderly patients and chemotherapy‐naive patients with poor performance status (PS).
Acupunch Exercise Program Development and Feasibility Evaluation for Older Adults.

PURPOSE The aim of the study was to develop the Healthy Beat Acupunch (HBA) exercise program and evaluate its feasibility for community older adults. DESIGN Stage I: The Delphi technique was used to consult 16 experts to develop the program. Stage II: A preexperimental, one-group, posttest-only design was used to pilot-test the program feasibility with 31 older adults. METHODS After 4 weeks of interventions, participants evaluated the program based on four criteria (simplicity, safety, suitability, and helpfulness) and responded to five open-ended questions. FINDINGS The developed HBA program from Stage I includes three phases with 24 motions and takes 40 minutes to complete. Program feasibility in Stage II showed average scores ranged from 8.84 ± 1.32 to 9.97 ± 0.18. CONCLUSION Both experts and elderly participants confirmed that the HBA program was simple, safe, suitable, and helpful to older adults. CLINICAL RELEVANCE The HBA program provides older adults with a new set of exercise option.
AUCTION MECHANISM TO ALLOCATE AIR TRAFFIC CONTROL SLOTS

This article deals with an auction mechanism for airspace slots, as a means of solving the European airspace congestion problem. A disequilibrium between air traffic control (ATC) services supply and ATC services demand are at the origin of almost one-fourth of delays in the air transport industry in Europe. In order to tackle this congestion problem, the authors suggest modifying both pricing and allocation of ATC services, by setting up an auction mechanism. Objects of the auction will be the right for airlines to cross a part of the airspace, and then to benefit from ATC services over a period corresponding to the necessary time for the crossing. Allocation and payment rules have to be defined according to the objectives of this auction. The auctioneer is the public authority in charge of ATC services, whose aim is to obtain an efficient allocation. Therefore the social value will be maximized. Another objective is to internalize congestion costs. To that end, we apply the principle of Clarke-Groves mechanism auction: each winner has to pay the externalities imposed on other bidders. The complex context of ATC leads to a specific design for this auction.
A case for hardware-supported sub-cache line accesses

Largely, the performance of main-memory databases is limited by the growing memory gap. To be efficient, a DBMS cannot waste any bandwidth. However, this is exactly the case when 64-byte cache lines are transferred but only parts of these are used. We present a cache simulator that measures this waste, show that current databases waste up to 70% of the available bandwidth, and discuss a new gather instruction with sub-cache line access granularity that could reduce this waste.
Meta Learner with Linear Nulling

We propose a meta-learning algorithm utilizing a linear transformer that carries out null-space projection of neural network outputs. The main idea is to construct an alternative classification space such that the error signals during few-shot learning are quickly zero-forced on that space so that reliable classification on low data is possible. The final decision on a query is obtained utilizing a null-space-projected distance measure between the network output and reference vectors, both of which have been trained in the initial learning phase. Among the known methods with a given model size, our meta-learner achieves the best or near-best image classification accuracies with Omniglot and miniImageNet datasets.
Magnetic Resonance Imaging and Interictal Electroencephalography Findings in Newly Diagnosed Epileptic Children

Introduction: Epilepsy is one of the most frequently diagnosed chronic neurological disorders in children. Diagnosis is often based on seizure history and electroencephalography (EEG) assessment. Magnetic resonance imaging (MRI) is recommended for etiologic workup and intervention requirements. We aimed to detect by MRI if focal structural abnormalities are present in the brain in relation to interictal epileptiform discharges (IED). Material and Methods: The study was designed retrospectively. The data were collected from patients admitted to Near East University, Department of Pediatric Neurology, who were aged between 3 months and 18 years and who were diagnosed with epilepsy. The cases considered in the current study, however, were patients that had an EEG record prior to initiating treatment and an MRI within the first six months following diagnosis. Results: Among 222 patients, 212 (95.5%) had IED, and 92 (41.4%) had abnormal MRI results. The most frequently seen abnormalities detected by MRI were encephalomalacia, hydrocephaly, and atrophy. Among patients who had IED, the ones with multifocal IED were documented to have a statistically significant higher rate of abnormalities in MRI scans. In other patients, IED had no significant correlation with structural lesions detected by MRI. Conclusion: IED can be unrelated to MRI findings. Focal IED were not statistically concordant with the structural lesions detected by MRI. However, for the cases with multifocal discharges revealed by interictal EEG, the rate of abnormalities detected using MRI was 68%. Therefore, the likelihood of detecting abnormalities using MRI in patients with multifocal IED does support the necessity of the use of MRI in early diagnosis stages.
Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer

Rationale: In lung cancer, upregulation of the PI3K (phosphoinositide 3‐kinase) pathway is an early event that contributes to cell proliferation, survival, and tissue invasion. Upregulation of this pathway was recently described as associated with enrichment of the lower airways with bacteria identified as oral commensals. Objectives: We hypothesize that host‐microbe interactions in the lower airways of subjects with lung cancer affect known cancer pathways. Methods: Airway brushings were collected prospectively from subjects with lung nodules at time of diagnostic bronchoscopy, including 39 subjects with final lung cancer diagnoses and 36 subjects with noncancer diagnoses. In addition, samples from 10 healthy control subjects were included. 16S ribosomal RNA gene amplicon sequencing and paired transcriptome sequencing were performed on all airway samples. In addition, an in vitro model with airway epithelial cells exposed to bacteria/bacterial products was performed. Measurements and Main Results: The composition of the lower airway transcriptome in the patients with cancer was significantly different from the control subjects, which included up‐regulation of ERK (extracellular signal‐regulated kinase) and PI3K signaling pathways. The lower airways of patients with lung cancer were enriched for oral taxa (Streptococcus and Veillonella), which was associated with up‐regulation of the ERK and PI3K signaling pathways. In vitro exposure of airway epithelial cells to Veillonella, Prevotella, and Streptococcus led to upregulation of these same signaling pathways. Conclusions: The data presented here show that several transcriptomic signatures previously identified as relevant to lung cancer pathogenesis are associated with enrichment of the lower airway microbiota with oral commensals.
Socio-economic factors and management regimes as drivers of tree cover change in Nepal

Despite the local and global importance of forests, deforestation is driven by various socio-economic and biophysical factors continues in many countries. In Nepal, in response to massive deforestation, the community forestry program has been implemented to reduce deforestation and support livelihoods. After four decades of its inception, the effectiveness of this program on forest cover change remains mostly unknown. This study analyses the spatial and temporal patterns of tree cover change along with a few socio-economic drivers of tree cover change to examine the effectiveness of the community forestry program for conserving forests or in reducing deforestation. We also investigate the socio-economic factors and policy responses as manifested through the community forestry program responsible for the tree cover change at the district level. The total tree cover area in the year 2000 in Nepal was ∼4,746,000 hectares, and our analysis reveals that between 2001 and 2016, Nepal has lost ∼46,000 ha and gained ∼12,200 ha of areas covered by trees with a substantial spatial and temporal variations. After accounting socio-economic drivers of forest cover change, our analysis showed that districts with the larger number of community forests had a minimum loss in tree cover, while districts with the higher proportion of vegetation covered by community forests had a maximum gain in tree cover. This indicates a positive contribution of the community forestry program to reducing deforestation and increasing tree cover.