Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic API Usage Scenario Documentation from Technical Q&A Sites

The online technical Q&A site Stack Overflow (SO) is popular among developers to support their coding and diverse development needs. To address shortcomings in API official documentation resources, several research works have thus focused on augmenting official API documentation with insights (e.g., code examples) from SO. The techniques propose to add code examples/insights about APIs into its official documentation. Recently, surveys of software developers find that developers in SO consider the combination of code examples and reviews about APIs as a form of API documentation, and that they consider such a combination to be more useful than official API documentation when the official resources can be incomplete, ambiguous, incorrect, and outdated. Reviews are opinionated sentences with positive/negative sentiments. However, we are aware of no previous research that attempts to automatically produce API documentation from SO by considering both API code examples and reviews. In this article, we present two novel algorithms that can be used to automatically produce API documentation from SO by combining code examples and reviews towards those examples. The first algorithm is called statistical documentation, which shows the distribution of positivity and negativity around the code examples of an API using different metrics (e.g., star ratings). The second algorithm is called concept-based documentation, which clusters similar and conceptually relevant usage scenarios. An API usage scenario contains a code example, a textual description of the underlying task addressed by the code example, and the reviews (i.e., opinions with positive and negative sentiments) from other developers towards the code example. We deployed the algorithms in Opiner, a web-based platform to aggregate information about APIs from online forums. We evaluated the algorithms by mining all Java JSON-based posts in SO and by conducting three user studies based on produced documentation from the posts. The first study is a survey, where we asked the participants to compare our proposed algorithms against a Javadoc-syle documentation format (called as Type-based documentation in Opiner). The participants were asked to compare along four development scenarios (e.g., selection, documentation). The participants preferred our proposed two algorithms over type-based documentation. In our second user study, we asked the participants to complete four coding tasks using Opiner and the API official and informal documentation resources. The participants were more effective and accurate while using Opiner. In a subsequent survey, more than 80% of participants asked the Opiner documentation platform to be integrated into the formal API documentation to complement and improve the API official documentation.
An Accurate P3M Algorithm for Gravitational Lensing Studies in Simulations

We present a two-dimensional particle–particle–particle-mesh (P3M) algorithm with an optimized Green’s function and adaptive softening length for gravitational lensing studies in N-body simulations. The analytical form of the optimized Green’s function Gˆ(k) is given. The softening schemes (S) are studied for both the particle-mesh (PM) and the particle–particle (PP) calculations in order for accurate force calculation and suppression of the particle discreteness effect. Our method is two orders of magnitude more accurate than the simple PM algorithm with the poor man’s Green’s function (∝ 1/k 2) at a scale of a few mesh cells or smaller. The force anisotropy is also much smaller than the conventional PM calculation. We can achieve a force accuracy better than 0.1% at all scales with our algorithm, which makes it an ideal (accurate and fast) algorithm for microlensing studies. When we apply the algorithm to computing weak and strong lensing quantities in N-body simulations, the errors are dominated by the Poisson noise caused by particle discreteness. The Poisson noise can be suppressed by smoothing out the particle distribution, which can be achieved by simply choosing an adaptive softening length in the PP calculation. We have presented a criterion to set the adaptive softening length. Our algorithm is also applicable to cosmological simulations. We provide a python implementation P3Mlens for this algorithm.
Swept Source Optical Coherence Tomography Compared to Ultrasound and Biomicroscopy for Diagnosis of Posterior Vitreous Detachment

Background Biomicroscopy, B-scan ultrasound imaging, and SD-OCT are all modalities used to characterize a posterior vitreous detachment (PVD). Our objective is to assess the precision of the diagnosis of PVD by SS-OCT. Methods This prospective observational study examines ninety-five eyes of forty-nine patients with biomicroscopy, B-scan ultrasound, and SS-OCT for the presence or absence of a complete PVD. All SS-OCT images were reviewed by two retina specialists (RWSC, ZM). All three diagnostic methods were evaluated for agreement by Cohen’s kappa statistic. Results The inter-rater reliability between retina specialists reading the SS-OCT images was 97.9% (κ = 0.957). Agreement on PVD status between SS-OCT and biomicroscopy was 85.3% (κ = 0.711). Agreement between SS-OCT and B-scan ultrasound was 83.2% (κ = 0.667). Agreement between B-scan ultrasound and biomicroscopy was 87.4% (κ = 0.743). Conclusion For the diagnosis of complete PVD, SS-OCT allows for high accuracy and agreement between graders.
Pomelo peel oil alleviates cerebral NLRP3 inflammasome activation in a cardiopulmonary resuscitation rat model

The NLR family pyrin domain-containing 3 (NLRP3) inflammasome, which is composed of NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC) and pro-caspase-1 protein complexes, is activated by the reactive oxygen species (ROS) that are associated with ischemia-reperfusion (I/R) and are involved in brain damage. Pomelo peel oil (PPO) exhibits antioxidant activity. However, it is unclear whether PPO is able to attenuate NLRP3 inflammasome-induced inflammation and pyroptosis. Healthy male Sprague-Dawley rats were subjected to 7 min of cardiac arrest via trans-esophageal electrical stimulation, followed by cardiopulmonary resuscitation (CPR). The rats were then treated with PPO prior to reperfusion for 24 h. Hematoxylin and eosin staining was used to evaluate brain tissue and cell damage. In the brain tissues, reactive oxygen species (ROS) were assayed, immunofluorescence was used to analyze the expression of NLRP3 and western blotting was performed to determine the expression levels of neuroenolase (NSE), NF-κB, interleukin-1β (IL-1β), gasdermin D (GSDMD) and the NLRP3 inflammasome. Treatment of the rats with PPO significantly decreased the pathological damage of the brain tissue and reduced the expression of NSE, production of ROS and secretion of NF-κB, NLRP3, IL-1β and GSDMD. In conclusion, these results demonstrate the ability of PPO to protect the brain against I/R injury in rats after CPR by a mechanism involving inhibition of the inflammation and pyroptosis mediated by NLRP3 inflammasome activation.
Ultrasonography of the larynx: Novel use during the SARS-CoV-2 pandemic (Review)

Few articles have been published on the subject of laryngeal ultrasonography. However, considering the increased power and accuracy of ultrasound technology, this imaging modality should be reevaluated. The present review aimed to increase the awareness of fellow specialists regarding the use of this imaging tool in healthcare units that do not benefit from onsite ear, nose and throat (ENT) service. We illustrate the ultrasonographic examination protocol for the larynx along with the relevant anatomic landmarks. We review cases with laryngeal tumoral pathology that underwent ultrasonographic examination for improved management. All findings were confirmed through computerized tomography (CT) and endoscopy performed by the ENT specialist. The ultrasound of the larynx has potential utility in diagnosis (e.g., laryngeal abnormalities, speech and swallowing abnormalities, identification of endotracheal tube placement), treatment (e.g., guidance of percutaneous tracheostomy and cricothyrotomy) and prognosis (e.g., prediction of postextubation stridor and difficult intubation). This imaging modality could be useful in the current SARS-CoV-2 pandemics in reducing the exposure to invasive maneuvers producing aerosol, such as endoscopy.
Valproate Reverses Mania-Like Behavior of Clockdelta19 Mouse and Alters Monoamine Neurotransmitters Metabolism in the Hippocampus

Background Mice with a deletion at exon 19 of the circadian locomotor output cycles Kaput gene (Clockdelta19) exhibit mania-like behavior and have been one of the most common animal models for bipolar disorder (BD). The predictive validity of the Clockdelta19 was investigated via studies using lithium previously. Determination of effects of other mood stabilizers on Clockdelta19 mouse would be helpful for better understanding of the mechanism underlined. Methods Wildtype (WT) and Clockdelta19 mice were treated with saline (n = 10 for WT and n=10 for Clockdelta19) or valproate (VPA) (n = 10 for WT and n=10 for Clockdelta19) for 10 days. The hyperactivity, anxiety-like behaviors and depression-like behaviors were tested. The concentration of monoamine neurotransmitters and their metabolites in the hippocampus of saline or VPA treated WT and Clockdelta19 mouse (n = 8 for each) were also determined. Results VPA can reverse hyperactivity, lower level of anxiety-like and depression-like behaviors of the Clockdelta19 mouse. Clockdelta19 mouse exhibited lower levels of serotonin (5-HT) and dopamine (DA) in right hippocampus compared to WT mouse. Chronic VPA treatment did not affect the levels of 5-HT and DA, but can reduce the level of levodopa (L-DOPA) in the right hippocampus of Clockdelta19 mouse. Conclusion Our results indicated that chronic VPA treatment can reverse the mania-like behaviors of the Clockdelta19 mouse and further consolidate the validity of the Clockdelta19 mouse as a model of BD. Monoamine neurotransmitters and their metabolites in the hippocampus are partly regulated by mutation of the Clock gene or VPA treatment.
The Psychological Experience and Intervention in Post-Acute COVID-19 Inpatients

Purpose COVID-19 patients faced first-hand the life-threatening consequences of the disease, oftentimes involving prolonged hospitalization in isolation from family and friends. This study aimed at describing the psychological intervention to address the psychological difficulties and issues encountered by the hospitalized post-acute COVID-19 patients in a rehabilitation setting. Patients and Methods Patients’ demographics, medical diagnosis, and neuro-psychological information were collected from March 2nd to May 12th, 2020. The main psychological issues and intervention strategies were collected. Results A total of 181 patients were hospitalized during this period. Among them, the 47.5% underwent psychological assessment (N=86; age: 74.58±13.39; 54.7% females). The most common psychological issues were acute stress disorders (18.6%), anxious and demoralization symptoms (26.7%), depression (10.5%%), and troublesome grief (8.1%). Once recovered from COVID-19, many patients were discharged home (38.4%), some received further rehabilitation in non-COVID-19 wards (41.9%), mostly due to pre-existent diseases (72.2%) rather than to COVID-19 complications (27.8%). Conclusion A great number of the hospitalized post-acute COVID-19 patients showed psychological issues requiring psychological intervention, the most common were anxiety, demoralization, acute stress, depression, and grief. The proposed psychological treatment for hospitalized COVID-19 patients was conducted in a Cognitive Behavioral framework. In particular, during the COVID-19 pandemic, psychological intervention is an important part of rehabilitation in the post-acute phase of the illness to reduce distress symptoms and improve psychological health.
Solving Copper Corrosion Problems while Maintaining Lead Control in a High Alkalinity Water Using Orthophosphate

Lead and Copper Rule sampling in 1992 uncovered high copper levels in many homes in the Indian Hill Water Works (Ohio) water system. The 90 th percentile copper and lead levels were 1.63 mg/L and 0.012 mg/L, respectively. Indian Hill Water Works (IHWW) supplies water to several suburban communities to the east of Cincinnati. Finished water hardness is approximately 150 mg/L as CaCO3, total alkalinity approximately 250 mg/L as CaCO3, DIC approximately 60-65 mg C/L, and pH ranges from about 7.1 to 7.5, mostly near 7.3. Final treatment consists of chlorination, fluoridation, and at different times, addition of caustic and/or corrosion inhibitor. Historically, water heater failures and high copper levels resulting in blue water were reported in the 1950’s, and caustic addition was used to elevate the pH to as high as 8 at different times throughout the next 3 decades. In the late 1980’s and early 1990’s, zinc orthophosphate treatment was employed, which was mostly successful for lead and inconsistently successful for copper. In 1997 with the 90th percentile still at 1.54 mg/L for copper, the zinc orthophosphate treatment was withdrawn. In 1998, new pilot tests were carried out in collaboration with the Water Supply and Water Resources Division of USEPA in Cincinnati to do some new pilot testing and a more systematic analysis of copper corrosion control chemistry. Tests compared pH adjustment, partial DIC removal through anion-exchange and increasing orthophosphate dosing. The most economical alternative identified was an increased orthophosphate residual of 3 mg/L as PO4. The recommended treatment was implemented beginning in 1999. Lead levels were below 0.005 mg/l for the 90 th percentile, and the 90 th percentile copper levels were reduced to 1.04 mg/L, for the fall 1999 and Spring 2000 sampling rounds. Copper levels remain consistently below the Action Level, and IHWW has now successfully met simultaneous lead and copper control requirements of the regulations and is now in “reduced monitoring” status.
Risk Perception of International Medical Students About Coronavirus (COVID-19) in China and Their Willingness to Fly Back

Purpose This study aimed to investigate the willingness of international medical students enrolled in Chinese universities to return to their home countries based on their risk perception of the recent outbreak of the novel coronavirus disease (COVID-19). Materials and Methods A well-structured questionnaire was incorporated into the WeChat survey, a special feature within this mobile application, similar to Google Docs. The questionnaire was sent to 1190 international medical students across China between January 1, 2020 and May 15, 2020. A total of 897 completed questionnaires were returned, indicating a 75% response rate. Results The survey findings show that the risk perception of international medical students about COVID-19 was low because of the strong preventive measures taken by the Chinese government against COVID-19. Moreover, they were willing to stay in China until the completion of their degrees. In contrast, students who have completed their degrees were willing to return home immediately if possible. Conclusion These findings are of serious concern for developing countries where they come from because their return to their home countries may cause an epidemic outbreak in those regions.
GATA1-Activated HNF1A-AS1 Facilitates the Progression of Triple-Negative Breast Cancer via Sponging miR-32-5p to Upregulate RNF38

Background Triple-negative breast cancer (TNBC) is a highly invasive subtype of breast cancer with a high mortality rate. Recently, long non-coding RNAs (lncRNAs) are confirmed to modulate the progression of assorted cancers, including TNBC. However, the functions of lncRNA HNF1 homeobox A antisense RNA 1 (HNF1A-AS1) in TNBC are still unclear. Aim We aimed to investigate the function and mechanism of HNF1A-AS1 in TNBC. Methods The expression of genes in TNBC cells was tested by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot. In vitro loss-of-function assays and in vivo xenograft experiments were conducted for evaluating the impact of HNF1A-AS1 on TNBC progression. RNA pull-down, luciferase reporter and RNA immunoprecipitation (RIP) assays were utilized for assessing the correlations between molecules. Results We discovered that HNF1A-AS1 was highly expressed in TNBC tissues and cells. Knockdown of HNF1A-AS1 restrained cell proliferation but accelerated cell apoptosis. Besides, GATA-binding protein 1 (GATA1) activated HNF1A-AS1 transcription in TNBC. MicroRNA-32-5p (miR-32-5p) was slowly expressed in TNBC cells and sponged by HNF1A-AS1, and its overexpression hinders TNBC cell growth. Ring finger protein 38 (RNF38) was verified as the target of miR-32-5p, and HNF1A-AS1 was a competing endogenous RNA (ceRNA) of RNF38 through sponging miR-32-5p. Rescue experiments indicated that upregulation of RNF38 reversed the inhibited impacts of silencing HNF1A-AS1 on TNBC cell growth. Conclusion GATA1-activated HNF1A-AS1 facilitated TNBC progression via miR-32-5p/RNF38 axis. The findings may provide new roads for developing targeted therapies of TNBC.
ER stress preconditioning ameliorates liver damage after hemorrhagic shock and reperfusion

The mismatch of oxygen supply and demand during hemorrhagic shock disturbs endoplasmic reticulum (ER) homeostasis. The resulting accumulation of unfolded proteins in the ER lumen, which is a condition that is defined as ER stress, triggers the unfolded protein response (UPR). Since the UPR influences the extent of organ damage following hemorrhagic shock/reperfusion (HS/R) and mediates the protective effects of stress preconditioning before ischemia-reperfusion injury, the current study investigated the mechanisms of ER stress preconditioning and its impact on post-hemorrhagic liver damage. Male C56BL/6-mice were injected intraperitoneally with the ER stress inductor tunicamycin (TM) or its drug vehicle 48 h prior to being subjected to a 90 min pressure-controlled hemorrhagic shock (30±5 mmHg). A period of 14 h after hemorrhagic shock induction, mice were sacrificed. Hepatocellular damage was quantified by analyzing hepatic transaminases and hematoxylin-eosin stained liver tissue sections. Additionally, the topographic expression patterns of the ER stress marker binding immunoglobulin protein (BiP), UPR signaling pathways, and the autophagy marker Beclin1 were evaluated. TM injection significantly increased BiP expression and modified the topographic expression patterns of the UPR signaling proteins. In addition, immunohistochemical analysis of Beclin1 revealed an increased pericentral staining intensity following TM pretreatment. The histologic analysis of hepatocellular damage demonstrated a significant reduction in cell death areas in HS/R+TM (P=0.024). ER stress preconditioning influences the UPR and alleviates post-hemorrhagic liver damage. The beneficial effects were, at least partially, mediated by the upregulation of BiP and autophagy induction. These results underscore the importance of the UPR in the context of HS/R and may help identify novel therapeutic targets.
Genetic diversity and structure of the narrow endemic Seseli farrenyi (Apiaceae): implications for translocation

Seseli farrenyi (Apiaceae) is an extremely narrow endemic plant, which is considered as one of the species of most conservation concern in Catalonia (NW Mediterranean Basin). Given the accelerated fragmentation and reduction of population size (of over 90%), the environmental agency of Catalonia is currently preparing a recovery plan that includes reinforcements of the extant populations. The present study is aimed at providing the necessary knowledge to carry out genetically-informed translocations, by using microsatellites as genetic markers. Fourteen microsatellites have been specifically developed for S. farrenyi, of which nine have been used. Besides the extant natural populations, the three ex situ collections that are known to exist of this species have also been studied, as they would be the donor sources for translocation activities. Our main finding is that levels of genetic diversity in the natural populations of S. farrenyi are still high (He = 0.605), most likely as a result of a predominantly outcrossing mating system in combination with the limited time elapsed since the population decline. However, population fragmentation is showing the first genetic signs, as the values of genetic differentiation are relatively high, and two well-differentiated genetic lineages have been found even in such a narrow geographic range. These genetic results provide important information when designing conservation management measures.
High expression of MCM10 is predictive of poor outcomes in lung adenocarcinoma

Backgrounds Lung adenocarcinoma is a complex disease that results in over 1.8 million deaths a year. Recent advancements in treating and managing lung adenocarcinoma have led to modest decreases in associated mortality rates, owing in part to the multifactorial etiology of the disease. Novel prognostic biomarkers are needed to accurately stage the disease and act as the basis of adjuvant treatments. Material and Methods The microarray datasets GSE75037, GSE31210 and GSE32863 were downloaded from the Gene Expression Omnibus (GEO) database to identify prognostic biomarkers for lung adenocarcinoma and therapy. The differentially expressed genes (DEGs) were identified by GEO2R. Functional and pathway enrichment analysis were performed by Kyoto Encyclopedia of Genes and Genomes and Gene Ontology (GO). Validation was performed based on 72 pairs of lung adenocarcinoma and adjacent normal lung tissues. Results Results showed that the DEGs were mainly focused on cell cycle and DNA replication initiation. Forty-one hub genes were identified and further analyzed by CytoScape. Here, we provide evidence which suggests MCM10 is a potential target with prognostic, diagnostic and therapeutic value. We base this on an integrated approach of comprehensive bioinformatics analysis and in vitro validation using the A549 lung adenocarcinoma cell line. We show that MCM10 overexpression correlates with a poor prognosis, while silencing of this gene decreases aberrant growth by 2-fold. Finally, evaluation of 72 clinical biopsy samples suggests that overexpression of MCM10 in the lung adenocarcinoma highly correlates with larger tumor size. Together, this work suggests that MCM10 may be a clinically relevant gene with both predictive and therapeutic value in lung adenocarcinoma.