Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematical Analysis of Circular RNAs in Triple Negative Breast Cancer

Background/Aims: This study aims to investigate circRNA expression profiles and their potential biological functions in Triple Negative Breast Cancer (TNBC). Methods: High-throughput RNA sequencing was used to assess circRNA expression profiles in TNBC, and Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) was used to validate dysregulated circRNA s. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to determine the biological functions of differentially expressed circRNA s. Bioinformatic analyses were applied to predict interactions between circRNA s and microRNAs (miRNAs), and a circRNA -miRNA-mRNA network was constructed using Cytoscape software. Results: We identified a number of differentially expressed circRNA s in TNBC tissues compared with paired normal tissues, with chr11:32589546:32596047:+, chr18:36195256:36203189:+, chr7:22266963:22318037:-, chr9:22046750:22064018:+, and chr10:836402:845055:being up regulated, and chr12: 55700898:55701154:-, chr15:54012647:54015886:+, chr5:55467868:55491114:, chr4:61934839:62044549:+ and chr7:152145152:152149152:being down regulated. These findings were confirmed by qRT-PCR. GO and KEGG pathway analyses showed that some of these circRNA s are related to cancers. Additionally, bioinformatic analyses revealed a potential competingendogenous-RNA-regulating network among circRNA s, miRNAs, and mRNAs. Conclusion: Our study results depict the landscape of circRNA expression profiles in TNBC and also provide potential biomarkers for TNBC. Further functional and mechanistic studies of this circRNA s may improve our understanding of TNBC tumorigenesis. Li XJ1, Yao YF1, Ren Z2, Bao J3* and Yu Q1 1Department of General Surgery, Jiangsu Cancer Hospital, China 2Department of Pathology, Jiangsu Cancer Hospital, China 3Department of Medical Oncology, Jiangsu Cancer Hospital, China
Neural Theorem Proving on Inequality Problems

We present an attempt to prove rudimentary inequality theorems as solving sequential decision making problems. Our contributions include 1. , designing an inequality theorem generator that can sample nontrivial inequality theorems of arbitrary length, given a set of axioms 2. demonstrating various degree of generalizations of a graph neural network based learning agent. We believe the proposed dataset can be used as a testbed for machine learning methods on theorem proving.
Clinicopathological Profile of Primary Mediastinal Masses: Our Experience

Background: Primary mediastinal masses are uncommon lesions encountered in clinical practice and the source of origin of these masses can be an enigma for the clinicians. These masses can be neoplastic, congenital, or inflammatory in nature. The data regarding their true incidence and the clinicopathological profile they present with is scarce due to their rarity. The clinical manifestations of these masses are usually nonspecific and protean. A standardized diagnostic workup is essential for their early detection and proper management. We retrospectively analyzed the clinicopathological profile of 29 cases of mediastinal masses diagnosed and operated in the department of General Surgery at a tertiary care hospital over a period of 11 years (2008-2019). Aims and objectives: The study aims to assess the clinical profile of adult patients with primary mediastinal masses that presented to General Surgery department at Government Medical College and Hospital, Chandigarh (India). Study design: This was a retrospective, descriptive and cross-sectional study of 11 years in which 29 patients of primary mediastinal masses with a definitive pathologic diagnosis after surgical resection were included. Detailed clinical profile, radiological and pathological findings along with their management outcome was noted. Results: Maximum numbers of cases were symptomatic at presentation and presented with non-specific symptoms. Maximum numbers of cases were found to be in the 3rd decade of life. Anterior mediastinal masses are encountered more frequent as compared to middle and posterior compartments. Male to female ratio was almost equivalent and benign tumor predominated in this study. Diagnostic workup included thorough radiological assessment using Chest X-Ray and Contrast Enhanced CT scan (CECT). FNAC and/or biopsy were performed as and when required. Final histopathological analysis after surgical resection revealed 6 cases of thymoma, 6 cases of teratoma, 5 cases of neurofibroma, 3 cases of retrosternal goitre, 2 benign epithelial cyst, 2 schwannoma, 1 case each of bronchogenic cyst, ganglioneuroma and chylo-lymphatic cyst. Conclusion: Majority of the patients of primary mediastinal masses present with non-specific chest pain and/or symptoms of compression at the time of their first visit to the hospital. Early detection is the key for prompt surgical intervention to reduce the overall morbidity associated with these masses.
Post-Traumatic Skin Lesion Caused by Scedosporium Apiospermum in an Immunocompetent Patient: Case Report

Scedosporium apiospermum is a saprophytic filamentous fungus that can cause infections of the skin, respiratory system, central nervous system, and bones. It affects mainly to immunosuppressed patients, but also and more rarely to immunocompetent patients. In these cases the organisms typically cause acute inflammation of the dermis or subcutaneous tissues, with erythema, subcutaneous nodules, and ulcer formation. The early diagnosis for this fungus is essential and voriconazole is an effective antifungal treatment, together with aggressive cleaning and surgical debridement. We report a S. apiospermum infection in a 77-year-old man who suffered a rabbit scratch in his left hand.
Foreign Body (FB) Insertion is a Common Presentation in Emergency Surgery and Gastroenterology

Background: Foreign Body (FB) insertion is common presentation in emergency surgery and gastroenterology; there are guidelines available for management of accidental insertion of FB. The primary aim of this study was to look at demography, common site of insertion, common operation for retrial of FB and documentation of mental health diagnosis in patients admitted with FB insertion on surgical ward. We also looked at the literature and discussed most common psychiatric diagnosis and there presentation in these patients. Method: We retrospectively analyzed data for all the patients admitted with diagnosis of FB in our hospital. The admission under general surgery, pediatrics, ENT and urology subspecialties were all included. Children with genital FB were excluded as they were transferred to pediatric surgery due to safeguarding issues. Retrospective data for last 4 year from January 2014 to January 2017 was collected using hospital electronic record system. Online e discharge summaries, operation theatre record and PACE radiology system was used to collect the date. Number of episodes of admission for each patient was recorded using online system. Patients were divided into accidental and MHI groups. MHI subgroup analysis was done to identify above mention characteristics. Results: A total of 146 patients with diagnosis of FB were admitted in above mentioned period. 57% (84) were with a diagnosis of accidental ingestion out of which 70% ( 54) were under the age of 16 years predominantly male with most common site of insertion was ENT. The commonest cause of accidental FB in adults was food bolus followed by fish bone. MHI group made 43% (63) of all the patients admitted with diagnosis of FB insertion. We recorded 257 episodes for these 63 patients, with maximum of 21 episodes in one patient. Mean age was 25 ± 21. Female sex and younger age group were at higher risk of ingestion. Oesophagus, stomach and skin were most common site of insertion in female patients with MHI while Stomach followed by rectum was most common site of insertion in male patients with MHI. AXR was most common investigation in these patients. Endoscopic retrieval was successful in 85% of patients with FB in GI, Urinary and respiratory track. Most of the patients with diagnosis of MHI were either under psychiatric care or were referred during their admission. Surprisingly Patient with rectal FB were not referred or seen by psychiatric services. Three deaths were recorded one in accidental and two in MHI secondary to complications arising from FBs ingestion. Conclusion: MHI patient are frequent attenders with recurrent presentations with FB ingestion in surgery or gastroenterology ward, their basic epidemiology and common presentation should be understood. Basic knowledge of common psychiatric problems among surgeons/medics can help during their acute admission on general ward. Early recognition and referral to mental health services can help and reduce future presentations.
Hematological indices in congenital hypogonadism and the effect of testosterone replacement therapy: A retrospective study

Patients with hypogonadism present with clinical findings of low testosterone levels such as low libido, loss of energy, depression, and muscle atrophy. In addition to fertility defects, the prevalence of type 2 diabetes, hypertension, and dyslipidemia is increased in patients with hypogonadism (1,2). Recent studies have also showed a relationship between low testosterone level and atherosclerosis, coronary artery disease, or cardiovascular (CV) events (3,4). Inflammation and thrombosis have important roles in the pathogenesis of atherosclerosis and CV diseases (CVD) (5). Testosterone deficiency is associated with metabolic profiles that are known to be associated with atherosclerosis such as high glucose, low DOI: 10.4274/gulhane.galenos. 2021.96268 ORIGINAL ARTICLE
Oncology nurses' perceived knowledge, assessment, and recommendation of alternative therapies

Oncology Nurses’ Perceived Knowledge, Assessment, and Recommendation of Alternative Therapies by Gudrun Kristofersdottir Dr. Cheryl L. Bowles, Examination Committee Chair Professor o f Nursing University o f Nevada, Las Vegas Cancer patients use alternative therapies (ATs) frequently and often without the knowledge o f their health care providers. The purpose o f this study was to investigate oncology nurses’ perceived knowledge of ATs, their level o f assessment of the use o f ATs by cancer patients, and what ATs they recommend to patients. The framework used to guide this study is the Neuman System Model. A descriptive survey design using a questiormaire listing 24 ATs was used to survey a random sample o f nurses certified by the Oncology Nurses Certification Corporation in the Western region o f the U.S. Results o f the survey (n=278) indicate that a majority o f participants perceived their knowledge of ATs to be average or above average (69.4%), 71% assessed at least sometimes the use o f ATs, and 56% recommended at least sometimes ATs to their patients. Participants were most knowledgeable about and recommended most frequently support groups, meditation/relaxation, prayer, imagery, and massage. Implications are discussed regarding the need for additional nursing education related to ATs.
The Moderating Role of Tangibility in Synchronous Innovation in Services

A synchronous pattern of innovation as between technological and management innovation, for example, can help firms improve their performance. This article explores this idea with respect to servitizing companies that introduce service delivery innovation as a means of gaining competitive advantage. It finds that the degree of tangibility, an indicator of the firm’s position on the product–service continuum, affects whether and how managers recognize the need for management innovation when introducing service delivery innovation. Using a socio‐technical perspective in conjunction with insights from managerial cognition, the relationship between management innovation and two central types of service delivery innovation—technological and customer interface—is examined. Tangibility shapes the managerial cognitive structures that are related to the enterprise’s technical and social subsystems in a paradigm that is capable of demonstrating contrasting effects. Technological delivery innovation is related to management innovation in firms with high tangibility. Customer interface delivery innovation, on the other hand, relates to management innovation in firms with low tangibility. This study uses a sample of diverse firms with varying degrees of tangibility to provide support for this theory.
Causally Linking Neural Dominance to Perceptual Dominance in a Multisensory Conflict

When different senses are in conflict, one sense may dominate the perception of other sense, but it is not known whether the sensory cortex associated with the dominant modality exerts directional influence, at the functional brain level, over the sensory cortex associated with the dominated modality; in short, the link between sensory dominance and neuronal dominance is not established. In a task involving audio-visual conflict, using magnetoencephalography recordings in humans, we first demonstrated that the neuronal dominance – visual cortex being functionally influenced by the auditory cortex – was associated with the sensory dominance – participants’ visual perception being qualitatively altered by sound. Further, we found that prestimulus auditory-to-visual connectivity could predict the perceptual outcome on a trial-by-trial basis. Subsequently, we performed an effective connectivity-guided neurofeedback electroencephalography experiment and showed that participants who were briefly trained to increase the neuronal dominance from auditory to visual cortex also showed higher sensory, i.e. auditory, dominance during the conflict task immediately after the training. The results shed new light into the interactive neuronal nature of multisensory integration and open up exciting opportunities by enhancing or suppressing targeted mental functions subserved by effective connectivity.
Effects of visual inputs on neural dynamics for coding of location and running speed in medial entorhinal cortex

Neuronal representations of spatial location and movement speed in the medial entorhinal cortex during the “active” theta state of the brain are important for memory-guided navigation and rely on visual inputs. However, little is known about how visual inputs change neural dynamics as a function of running speed and time. By manipulating visual inputs in mice, we demonstrate that changes in spatial stability of grid cell firing as a function of time correlate with changes in a proposed speed signal by local field potential theta frequency. In contrast, visual inputs do not affect the speed modulation of firing rates. Moreover, we provide evidence that sensory inputs other than visual inputs can support grid cell firing, though less accurately, in complete darkness. Finally, changes in spatial accuracy of grid cell firing on a 10-s time scale suggest that grid cell firing is a function of velocity signals integrated over past time.
Three-Dimensional Motion Perception: Comparing Speed and Speed Change Discrimination for Looming Stimuli

Judging the speed of objects moving in three dimensions is important in our everyday lives, because we interact with objects in a three-dimensional world. However, speed perception has been seldom studied for motion in depth, particularly when using monocular cues such as looming. Here, we compared speed discrimination, and speed change discrimination, for looming stimuli, to better understand what visual information is used for these tasks. For the speed discrimination task, we manipulated the distance and duration information available, to investigate if participants were specifically using speed information. For speed change discrimination, total distance and duration were held constant, hence they could not be used to successfully perform that task. We found speed change discrimination thresholds were consistently higher than those for speed discrimination. Evidence suggested that participants used a variety of cues to complete the speed discrimination task, not always solely relying on speed. Further, our data suggested that participants may switch between cues on a trial to trial basis. We conclude that speed change discrimination for looming is more difficult than speed discrimination, and that naїve participants may not always exclusively use speed for speed discrimination.
Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.
Genetic diversity of Anopheles coustani in high malaria transmission foci in southern and central Africa

Despite ongoing malaria control efforts implemented throughout sub-Saharan Africa, malaria remains an enormous public health concern. Current interventions such as indoor residual spraying with insecticides and use of insecticide-treated bed nets are aimed at targeting the key malaria vectors that are primarily endophagic and endophilic. While these control measures have resulted in a substantial decline in malaria cases and continue to impact indoor transmission, the importance of alternative vectors for malaria transmission has been largely neglected. Anopheles coustani, an understudied vector of malaria, is a species previously thought to exhibit mostly zoophilic behavior. However, recent studies from across Africa bring to light the contribution of this and ecologically similar anopheline species to human malaria transmission. Like many of these understudied species, An. coustani has greater anthropophilic tendencies than previously appreciated, is often both endophagic and exophagic, and carries Plasmodium falciparum sporozoites. These recent developments highlight the need for more studies throughout the geographic range of this species and the potential need to control this vector. The aim of this study was to explore the genetic variation of An. coustani mosquitoes and the potential of this Anopheles species to contribute to malaria parasite transmission in high transmission settings in Nchelenge District, Zambia, and the Kashobwe and Kilwa Health Zones in Haut-Katanga Province, the Democratic Republic of the Congo (DRC). Morphologically identified An. coustani specimens that were trapped outdoors in these study sites were analyzed by PCR and sequencing for species identification and blood meal sources, and malaria parasite infection was determined by ELISA and qPCR. Fifty specimens were confirmed to be An. coustani by the analysis of mitochondrial DNA cytochrome c oxidase subunit I (COI) and ribosomal internal transcribed spacer region 2 (ITS2). Further, maximum likelihood phylogenetic analysis of COI and ITS2 sequences revealed two distinct phylogenetic groups within this relatively small regional collection. Our findings indicate that both An. coustani groups have anthropophilic and exophagic habits and come into frequent contact with P. falciparum, suggesting that this potential alternative malaria vector might elude current vector controls in Northern Zambia and Southern DRC. This study sets the groundwork for more thorough investigations of bionomic characteristics and genetic diversity of An. coustani and its contribution to malaria transmission in these regions.
Tissue-specific multi-omics analysis of atrial fibrillation

Genome-wide association studies (GWAS) for atrial fibrillation (AF) have uncovered numerous disease-associated variants. Their underlying molecular mechanisms, especially consequences for mRNA and protein expression remain largely elusive. Thus, refined multi-omics approaches are needed for deciphering the underlying molecular networks. Here, we integrate genomics, transcriptomics, and proteomics of human atrial tissue in a cross-sectional study to identify widespread effects of genetic variants on both transcript (cis-eQTL) and protein (cis-pQTL) abundance. We further establish a novel targeted trans-QTL approach based on polygenic risk scores to determine candidates for AF core genes. Using this approach, we identify two trans-eQTLs and five trans-pQTLs for AF GWAS hits, and elucidate the role of the transcription factor NKX2-5 as a link between the GWAS SNP rs9481842 and AF. Altogether, we present an integrative multi-omics method to uncover trans-acting networks in small datasets and provide a rich resource of atrial tissue-specific regulatory variants for transcript and protein levels for cardiovascular disease gene prioritization. Numerous disease-associated variants have been described in GWAS for atrial fibrillation. Here the authors integrate omics data to investigate the consequences of genetic variants for transcript and protein levels in the atrium of the human heart. With this multi-omics approach, authors reveal the regulatory network underlying atrial fibrillation and provide a resource for cardiac gene prioritization.
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Identifying chromatin domains (CDs) from high-throughput chromosome conformation capture (Hi-C) data is currently a central problem in genome research. Here we present a unified algorithm, Multi-CD, which infers CDs at various genomic scales by leveraging the information from Hi-C. By integrating a model of the chromosome from polymer physics, statistical physics-based clustering analysis, and Bayesian inference, Multi-CD identifies the CDs that best represent the global pattern of correlation manifested in Hi-C. The multi-scale intra-chromosomal structures compared across different cell types allow us to glean the principles of chromatin organization: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by different organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. CDs obtained from Multi-CD applied to Hi-C data enable a quantitative and comparative analysis of chromosome organization in different cell types, providing glimpses into structure-function relationship in genome.