Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining TCGA database for screening and identification of hub genes in kidney renal clear cell carcinoma microenvironment

To evaluate the diagnosis and prognosis of the tumor microenvironment (immunization and stromal cells) in kidney renal clear cell carcinoma (KIRC), KIRC cases selected from The Cancer Genome Atlas database were divided into two groups according to the ESTIMATE algorithm‐derived immune scores. Our data suggested that the Von Hippel‐Lindau mutations and pathologic grades are associated with immune scores. Importat ntly, we identified 173 differential expression genes (DEGs) associated with prognosis in patients with KIRC. Consequently, Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed on these DEGs, which included immune response, defense response, intrinsic to the plasma membrane, positive regulation of immune system process, and cytokine binding. Next, the protein‐protein interaction network of DEGs and the most significant module was constructed. Five hub genes were identified and analyzed using biological analysis. The survival analysis of the hub genes showed that KIRC patients with high gene expression of C2, MXRA8, TNFSF13B, and X‐linked inhibitor of apoptosis protein‐associated factor 1 (XAF1) had worse overall survival, and MXRA8, TNFSF13B, and XAF1 alteration were significantly associated with disease‐free survival (DFS). In addition, high gene expression of XAF1 alteration showed better DFS. Conclusion: we identified a list of microenvironment‐related genes that are useful for understanding the molecular mechanisms and prognosis of KIRC.
The Impact of Infertility on Daily Occupations and Roles

Background: Infertility impacts approximately 16% of couples in the United States-roughly five million individuals. Experiencing infertility takes a physical and psychological toll on the infertile individual, as well as his/her partner. The goal of the current study was to explore and provide better insight into how infertility affects the roles and daily occupations (Such as self-care and work related tasks) of females. This information can better assist health care providers in providing quality care to such clients. Methods: 21 participants, females ranging in age from 20 to 46 years and experiencing infertility, participated in this qualitative, phenomenological research study. They partook in two telephone interviews aimed at exploring how infertility has impacted their roles and daily occupations. Inductive content data analysis was utilized to analyze the data. Results: Findings resulted in three main themes. Quotes from participants were used to title the themes. They are “when you’re dealing with infertility, every aspect of your life is impacted by it”, “infertility impacted my areas of interest in life” and “infertility is very lonely”. Conclusion: Infertility has the potential to impact every area of a female’s life. The emotional impact infertility may have on women, in addition to the physical and time constraints involved with pursuing fertility treatments, frequently resulted in decreased occupational engagement and fulfillment of roles as spouse or friend. Those experiencing infertility need more resources and support to navigate their journey.
Treatment choice in metaplastic breast cancer: A report of 5 cases

Metaplastic breast carcinoma (MBC) is a general term defining a heterogeneous group that includes biphasic lesions, with both malignant epithelial and mesenchymal tissue components. Although its clinical findings are similar to those present in invasive ductal carcinoma, it rarely presents with the findings of inflammatory breast cancer. It is generally seen in the fifth decade. MBC spreads via lymph and blood circulation. Most common distant metastasis areas include lungs and the bone. Although the treatment generally relies on the same principles applied in invasive ductal carcinoma, a more aggressive treatment should be employed in at-risk groups due to higher rates of local recurrence. In this study, we aimed to discuss clinicopathological features and treatment approach in 5 women with MBC.
Bradyarrhythmia development and permanent pacemaker implantation after cardiac surgery

OBJECTIVE: Bradyarrhythmia is one of the complications that may develop after cardiac surgery. Only a few studies have previously dealt with this concern, and in our study, we investigated the factors affecting the development of atrioventricular block or sinus node dysfunction and the requirement of permanent pacemaker following cardiac surgery. METHODS: A total of 62 patients who developed the atrioventricular (AV) block or sinus node dysfunction and required a permanent pacemaker following cardiac surgery were included in the study. Among these, 31 patients were evaluated prospectively, and the information regarding 31 patients was evaluated retrospectively based on hospital records. Demographic, clinical, and surgical information was recorded. Patients were grouped according to the types of procedures, including the coronary artery bypass graft, valve surgery, congenital heart disease, and combinations of these. Patients were evaluated by standard 12-lead electrocardiogram and transthoracic echocardiography preoperatively. The postoperative development of bradyarrhythmia and requirement of permanent pacemaker were evaluated. RESULTS: The mean age of patients with preoperative conduction abnormality and wide QRS was statistically significantly higher than those without these disorders. The odds ratio for preoperative conduction abnormality risk in patients over 70 years of age was found as 4.429 (95% confidence interval, 1.40–13.93). There was no gender-related statistically significant difference in terms of left ventricular ejection fraction, left ventricular dilatation, interventricular septum thickness, the time interval from operation to the development of AV block, concomitant diseases, and complication rates. CONCLUSION: Preoperative conduction abnormality and wide QRS in patients over 70 years of age was determined as a risk factor.
Fusion of Clinical, Self-Reported, and Multisensor Data for Predicting Falls

Falls are among the frequent causes of the loss of mobility and independence in the elderly population. Given the global population aging, new strategies for predicting falls are required to reduce the number of their occurrences. In this study, a multifactorial screening protocol was applied to 281 community-dwelling adults aged over 65, and their 12-month prospective falls were annotated. Clinical and self-reported data, along with data from instrumented functional tests, involving inertial sensors and a pressure platform, were fused using early, late, and slow fusion approaches. For the early and late fusion, a classification pipeline was designed employing stratified sampling for the generation of the training and test sets. Grid search with cross-validation was used to optimize a set of feature selectors and classifiers. According to the slow fusion approach, each data source was mixed in the middle layers of a multilayer perceptron. The three studied fusion approaches yielded similar results for the majority of the metrics. However, if recall is considered to be more important than specificity, then the result of the late fusion approach providing a recall of $\text{78.6}\%$ is better compared with the results achieved by the other two approaches.
Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae

Metagenomic sequencing of fecal DNA can usefully characterise an individual’s intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producing Enterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes in Enterobacteriaceae by using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer feces were spiked with carbapenemase-producing Enterobacteriaceae and incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a fecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.
SecTEE: A Software-based Approach to Secure Enclave Architecture Using TEE

Secure enclaves provide a practical solution to secure computation, and current approaches to secure enclaves are implemented by extending hardware security mechanisms to the CPU architecture. Therefore, it is hard for a platform to offer secure computation if its CPU architecture is not equipped with any secure enclave features. Unfortunately, ARM CPUs, dominating mobile devices and having increasing momentum in cloud markets, do not provide any security mechanisms achieving the security equivalent to modern secure enclave architectures. In this paper, we propose SecTEE, a software-based secure enclave architecture which is based on the CPU's isolation mechanism and does not require specialized security hardware of the CPU architecture such as memory encryption engines. SecTEE achieves a high level of security even compared with hardware-based secure enclave architectures: resistance to privileged host software attacks, lightweight physical attacks, and memory access based side-channel attacks. Besides, SecTEE provides rich trusted computing primitives for enclaves: integrity measurement, remote attestation, data sealing, secrets provisioning, and life cycle management. We implement a SecTEE prototype based on the ARM TrustZone technology, but our approach can be applied to other CPU architectures with isolation mechanisms. The evaluation results show that most overhead comes from the software encryption and the runtime overhead imposed by trusted computing primitives is acceptable.
Stimuli may have little impact on the deficit of visual working memory accuracy in first-episode schizophrenia

Purpose Working memory (WM) deficits have been observed in people with schizophrenia (SZ) and are considered a core cognitive dysfunction in these patients. However, little is known about how stimuli and memory load influence visual WM deficits. Patients and methods In the present study, we adopted a match-to-sample task to examine the visual WM in 18 first-episode patients with SZ and 18 healthy controls (HCs). Faces and houses were used as the stimuli, and there were two levels of memory load – one item and two items; the average accuracy (ACC) and reaction time were calculated for each condition. The Positive and Negative Syndrome Scale and the Personal and Social Performance scale were used to assess the psychiatric symptoms and social function, respectively. Results The results showed equivalent levels of WM deficit when using face and house stimuli. Moreover, the WM deficits were not related to the duration of illness, medication, or SZ symptoms. Conclusion These results demonstrate that stimuli may have little impact on ACC in WM tasks in people with SZ. In addition, the memory load may have little impact on WM ACC when the load is relatively low.
OCT-guided Percutaneous Coronary Intervention in Bifurcation Lesions

Coronary artery bifurcation lesions remain challenging despite significant advancements in stent technology and development of specific bifurcation stenting approaches. Optical coherence tomography (OCT) is the intracoronary imaging technique with the highest resolution and can generate automatically contoured lumen areas across the variable geometry of bifurcation lesions. Knowledge of plaque severity and composition facilitates planning of the best strategy for percutaneous coronary intervention (PCI) and stenting. In particular, the provisional stent strategy preferred in this context can be modified when there is high risk of side-branch compromise at the ostium after main vessel stenting. OCT is unique because it allows the identification of the site of guide wire crossing, an important determinant of the final result. OCT can also be used to assess the procedural success of new dedicated bifurcation stent technologies and for the evaluation at follow-up of potential predictors of stent thrombosis, including stent malapposition, stent under-expansion and stent-edge dissection. Finally, the development of 3D OCT allows a better evaluation of coronary anatomy — particularly of side branch ostium that is difficult to visualise by 2D OCT — further improving the value of this technique in guiding PCI in these patients.
Net Clinical Benefit of Oral Anticoagulation Among Older Adults With Atrial Fibrillation.

BACKGROUND While guidelines recommend anticoagulation for all atrial fibrillation (AF) patients ≥75 years, evidence for the net clinical benefit (NCB) of anticoagulant in older adults is sparse. We sought to determine the association between age and NCB of anticoagulation in older adults with AF. METHODS AND RESULTS We examined adults ≥75 years with incident AF in the Anticoagulation and Risk Factors in Atrial Fibrillation-Cardiovascular Research Network cohort. Using a Markov state transition model, we estimated the lifetime NCB of warfarin and apixaban relative to no treatment in quality-adjusted life years (QALYs). In the decision model, each month patients face a chance of stroke, hemorrhage, or death from a competing cause; the likelihood of each is a function of individual patients' stroke risk, hemorrhage risk, and life expectancy. We defined minimal clinically relevant lifetime benefit as 0.10 QALYs. In a sensitivity analysis, we examined the effect of competing risks of death on NCB using 2 models, one including competing risks and the second without competing risks. We included 14 946 patients, with a median age of 81 years and median CHA2DS2-VASc score of 4. In the main analysis, after age 87, NCB associated with warfarin decreased below 0.10 lifetime QALYs while NCB associated with apixaban did not decrease below 0.10 lifetime QALYs until after age 92. In sensitivity analyses, over a 3-year horizon, removing competing risks of death resulted in higher NCB (at 90 years, median difference using warfarin 0.010 QALYs [95% CI, 0.009-0.013], median difference using apixaban 0.025 QALYs [95% CI, 0.024-0.026]). CONCLUSIONS The NCB of anticoagulation decreases with advancing age. The competing risk of death diminishes the NCB of anticoagulation for older patients with AF. Physicians should consider competing mortality risks when recommending anticoagulants to older adults with AF.
Role of problem-based learning in undergraduate dental education: a questionnaire-based study

Background There is a debate regarding the significance of problem-based learning (PBL) model in educational systems. The aim of this study was to assess the awareness of dental students at the Princess Nourah Bint Abdulrahman University (PNU), Saudi Arabia, toward PBL. Methods The present cross-sectional study was performed at the College of Dentistry, PNU, Riyadh, Saudi Arabia. An anonymous, standardized and self-administered questionnaire (based on nine items) coded as 1, 2, 3 and 4 was distributed to the first-, second-, third- and fourth-year undergraduate students, respectively, after a seminar that focused on the perceptions of PBL among the students at the end of the academic year 2017. The questionnaire was developed following an exhaustive search of indexed databases. Based on the students’ responses (yes/no) to the questions, group mean differences (95% CI) were computed and Pearson’s chi-squared test was used for data analysis. Cronbach’s alpha coefficient was also determined. The level of significance was set at P<0.05. Results In total, 238 female undergraduate dental students (61 first-year, 59 second-year, 60 third-year and 58 fourth-year students) were included. The Cronbach’s alpha coefficient ranged between 0.82 and 0.93. Group comparisons (95% CI) showed no statistically significant difference in the responses (yes) of students in the first, second, third and fourth year of academic years related to the perceptions listed earlier (P>0.05). Conclusion Perception of female undergraduate dental students at the PNU was inconclusive. Further studies are warranted in this regard.
Self-declared Throwaway Accounts on Reddit

Parents can be subjected to scrutiny and judgment for their parenting choices. Much of this scrutiny is experienced online, especially around stigmatized topics such as divorce, custody, postpartum depression, and miscarriage. Prior theory suggests that parents might be able to access greater support online when anonymous, but other evidence suggests that anonymity may increase bad behavior. Drawing from ten years of Reddit parenting boards, we show that parents are more likely to discuss potentially stigmatizing topics using anonymous ("throwaway") accounts. We find that, on average, throwaway comments are more likely to receive a response, receive more responses that are longer, and receive responses that have higher karma scores than topically similar comments posted by non-throwaway accounts. We argue that self-identified throwaway accounts provide a crucial environment for supporting parents with stigmatizing experiences. They also provide a shared platform signal (the throwaway account) which enables other Reddit users to access shared experiences and support. We propose that a hybrid combination of identified and anonymous platforms could provide more supportive online experiences for parents and other users.
Adenovirus based virus-like-vaccines targeting endogenous retroviruses can eliminate growing colorectal cancers in mice

Endogenous retroviruses (ERVs) that make up 8% of the human genome have been associated with the development and progression of cancer. The murine model system of the melanoma associated retrovirus (MelARV), which is expressed in different murine cancer cell lines, can be used to study mechanisms and therapeutic approaches against ERVs in cancer. We designed a vaccine strategy (Ad5-MelARV) of adenoviruses encoding the MelARV proteins Gag and Env that assemble in vivo into virus-like particles displaying the cancer-associated MelARV Env to the immune system. The novel vaccine was designed to induce both humoral as well as cellular immune responses in order to attack ERV expressing tumor cells. Despite a lack of antibody induction, we found that T cell responses were strong enough to prevent colorectal CT26 tumor growth and progression in BALB/c mice after a single vaccination before or after tumor challenge. A combination with the checkpoint inhibitor anti-PD-1 further increased the efficacy of the vaccination leading to complete tumor regression. Furthermore, immune responses in vaccinated mice were not restricted to only one cancer cell line but vaccinated animals were also protected from a rechallenge with the distinct breast cancer cell line 4T1. Thus, the developed vaccine strategy could represent a novel tool to successfully target diverse ERV-bearing tumors in cancer patients.
When the Conventional Treatment Fails: A Rare Approach to Superior Mesenteric Arterial Embolization

Retroperitoneal haemorrhage is a rare but potentially life-threatening event. It may occur either spontaneously or secondary to percutaneous vascular access procedures, trauma, or ruptured aortic, iliac, or mesenteric aneurysms. As a result, the clinical presentation is variable. Computed tomography and/or angiography are vital for diagnosis. Management may range from conservative treatment for stable patients to emergency laparotomy or embolization for catastrophic haemorrhage. Direct percutaneous puncture of a deep intra-abdominal pseudoaneurysm is an accepted but infrequently performed technique due to a number of diagnostic and technical challenges. We describe the successful percutaneous transabdominal angioembolization of a superior mesenteric artery rupture in a 77-year-old woman with a large retroperitoneal haematoma. This was performed after a conventional femoral transarterial approach was unsuccessful.
Aberrant attentive and inattentive brain activity to auditory negative words, and its relation to persecutory delusion in patients with schizophrenia

Background and purpose Previous research has suggested that deficits in emotion recognition are involved in the pathogenesis of persecutory delusion in schizophrenia. Although disruption in auditory and language processing is crucial in the pathophysiology of schizophrenia, the neural basis for the deficits in emotion recognition of auditorily presented language stimuli and its relation to persecutory delusion have not yet been clarified. Patients and methods The current functional magnetic resonance imaging study used a dichotic listening task for 15 patients with schizophrenia and 23 healthy controls matched for age, sex, parental socioeconomic background, handedness, dexterous ear, and intelligence quotient. The participants completed a word recognition task on the attended side in which a word with emotionally valenced content (negative/neutral) was presented to one ear and a different neutral word was presented to the other ear. Participants selectively attended to either ear. Results The whole brain analysis detected the aberrant neural activity in the right inferior frontal gyrus in the patients with schizophrenia compared to that in the controls (P<0.05, false discovery rate-corrected). Brain activity in the right pars triangularis of the inferior frontal gyrus was significantly reduced when negatively valenced words were presented to the right ear, whereas the activity of the same region was significantly enhanced when these words were presented to the left ear, irrespective of the attended ear, in the participants with schizophrenia compared to the controls. Furthermore, this diminished brain response to auditorily presented negatively valenced words significantly correlated with severe positive symptoms (r=−0.67, P=0.006) and delusional behavior (r=−0.62, P=0.014) in the patients with schizophrenia. Conclusion The present results indicate that the significantly impaired brain activity in response to auditorily presented negatively valenced words in the right pars triangularis of the inferior frontal gyrus is associated with the pathogenesis of positive symptoms such as persecutory delusion.