Miracle-dz/UniFAR-FTUs huggingface dataset:
Transformed Follicular Lymphoma (TFL) Predicts Outcome in Advanced Endometrial Cancer

Background: Transformed follicular lymphoma (TFL, ZC3H12D) was identified as a candidate tumor suppressor gene that contributes to cell-cycle arrest through regulation of Rb phosphorylation, but the clinical impact of TFL is unknown. The goal of this study was to evaluate the prognostic significance of TFL expression in advanced endometrial cancer. Methods: Tissue samples were obtained from 103 patients with Federation Internationale des Gynaecologistes et Obstetristes stage III–IV endometrial cancer. Associations between TFL expression and outcomes were evaluated using the Kaplan–Meier method and multivariate Cox proportional hazards regression models. Results: There were 24 TFL-low cases (23.3%) and the 10-year progression-free survival (PFS) and overall survival (OS) in these cases were lower than those for patients with normal TFL expression in univariate analysis (PFS, P = 0.003; OS, P = 0.106). In multivariate analysis, TFL status was a significant predictor for PFS [HR = 2.76; 95% confidence interval (CI), 1.45–5.28; P = 0.002] and OS (HR = 1.94; 95% CI, 0.91–4.11; P = 0.085), adjusted for covariates. The TFL gene maps to human chromosome 6q25.1, where estrogen receptor alpha (ERα) gene ESR1 is also located. Lack of ERα expression is a poor prognostic factor in early endometrial cancer. Among 41 ERα-low patients, 10-year PFS was significantly lower in 15 TFL-low cases (univariate analysis, P = 0.055; multivariate analysis, HR = 4.70; 95% CI, 1.68–13.20; P = 0.003). Conclusions: We identified TFL as a strong independent prognostic factor, regardless of ERα status. Impact: An investigation of the mechanism underlying tumor suppression by TFL may lead to new therapies for patients with advanced endometrial cancer. Cancer Epidemiol Biomarkers Prev; 27(8); 963–9. ©2018 AACR.
Perception of social interaction compresses subjective duration in an oxytocin-dependent manner

Communication through body gestures permeates our daily life. Efficient perception of the message therein reflects one’s social cognitive competency. Here we report that such competency is manifested temporally as shortened subjective duration of social interactions: motion sequences showing agents acting communicatively are perceived to be significantly shorter in duration as compared with those acting noncommunicatively. The strength of this effect is negatively correlated with one’s autistic-like tendency. Critically, intranasal oxytocin administration restores the temporal compression effect in socially less proficient individuals, whereas the administration of atosiban, a competitive antagonist of oxytocin, diminishes the effect in socially proficient individuals. These findings indicate that perceived time, rather than being a faithful representation of physical time, is highly idiosyncratic and ingrained with one’s personality trait. Moreover, they suggest that oxytocin is involved in mediating time perception of social interaction, further supporting the role of oxytocin in human social cognition.
Hypoxia Induces Hypoxia-Inducible Factor 1α and Potential HIF-Responsive Gene Expression in Uterine Leiomyoma

Uterine leiomyoma is characterized by abundant extracellular matrix and broad avascular areas, both constantly resulting in hypoxia, suggesting some hypoxia-induced response function. Here, we examined whether hypoxia-inducible factor 1α (HIF-1α)- mediated hypoxic response function in uterine leiomyoma. Immunoblotting detected higher basal HIF-1α protein expression in nuclear extracts from uterine leiomyoma tissues than in those from the adjacent myometrium (P = .0011). Immunohistochemical analysis revealed the presence of HIF-1α-positive cellular components in both leiomyoma and surrounding myometrial tissues. Hypoxia decreased HIF-1α messenger RNA (mRNA), but increased HIF-1α protein in primary culture leiomyoma smooth muscle cells, and caused translocation of HIF-1α from the cytoplasm to the nucleus. Hypoxia upregulated mRNAs of 6 potential HIF-responsive genes (ALDOA, ENO1, LDHA, VEGFA, PFKFB3, and SLC2A1). Chromatin immunoprecipitation quantitative polymerase chain reaction revealed that hypoxia significantly increased recruitment of HIF-1α binding to putative HIF-responsive elements in the HIF-responsive genes, suggesting that the HIF transcriptional complex initiates hypoxia-induced transcription of HIF-responsive genes. These results demonstrated a HIF-1α-mediated hypoxic response in uterine leiomyoma.
A Noble Feature Selection Method for Human Activity Recognition using Linearly Dependent Concept (LDC)

Human physical activity recognition process using mobile phones is very complicated with many extracted features in which some features are irrelevant or redundant. Removing irrelevant or redundant features is not only reducing the dataset size but also saving the time consuming task. Hence, a reason to pick out the effective and useful features is our main study. We propose a noble feature selection technique using Linearly Dependent Concept (LDC). Our proposed work attempts a new feature selection method on UCI-HAR dataset. For classification, we use the feed forward neural network and compare the performance result with the original dataset. The goal of our study is not only to find an effective and useful features set from the original dataset but also to be better performance than original dataset. Finally, the experimental result of proposed method gives 2.7% more accuracy and reduces the relative error up to 2.67% of the original dataset.
Counterexample-Driven Genetic Programming: Heuristic Program Synthesis from Formal Specifications

Conventional genetic programming (GP) can guarantee only that synthesized programs pass tests given by the provided input-output examples. The alternative to such a test-based approach is synthesizing programs by formal specification, typically realized with exact, nonheuristic algorithms. In this article, we build on our earlier study on Counterexample-Based Genetic Programming (CDGP), an evolutionary heuristic that synthesizes programs from formal specifications. The candidate programs in CDGP undergo formal verification with a Satisfiability Modulo Theory (SMT) solver, which results in counterexamples that are subsequently turned into tests and used to calculate fitness. The original CDGP is extended here with a fitness threshold parameter that decides which programs should be verified, a more rigorous mechanism for turning counterexamples into tests, and other conceptual and technical improvements. We apply it to 24 benchmarks representing two domains: the linear integer arithmetic (LIA) and the string manipulation (SLIA) problems, showing that CDGP can reliably synthesize provably correct programs in both domains. We also confront it with two state-of-the art exact program synthesis methods and demonstrate that CDGP effectively trades longer synthesis time for smaller program size.
Fluid Extravasation in Shoulder Arthroscopic Surgery: A Systematic Review

Background: Arthroscopic surgery of the shoulder joint has become increasingly more common given its advantages over open surgery; however, one rare but potentially life-threatening complication is fluid extravasation into the surrounding tissues, causing edema, respiratory compromise, abnormal results on laboratory blood tests, and possibly death. Currently, no systematic review exists that summarizes the existing clinical research on this topic. Purpose: To perform a systematic review on fluid extravasation as a complication of shoulder arthroscopic surgery, specifically assessing clinical presentation, risk factors, management, and outcomes. Study Design: Systematic review; Level of evidence, 4. Methods: Two reviewers independently searched 3 databases (PubMed, Ovid [MEDLINE], and Embase) from database inception until July 1, 2017. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) checklist guided the reporting and data abstraction. The methodological quality of these studies was assessed using the Methodological Index for Non-Randomized Studies (MINORS) checklist. The results are presented in a narrative summary fashion using descriptive statistics including ranges and agreement statistics. Results: A total of 26 studies (20 case reports, 4 case series, and 2 prospective comparative studies) encompassing 205 patients (mean age, 50.8 years [range, 15-83 years]) were included. The most common signs of fluid extravasation included chest wall swelling (n = 86) and neck swelling (n = 116). In 32 patients, observation alone was sufficient. Other patients required airway intubation (n = 16), diuretics (n = 7), steroids (n = 1), and percutaneous drainage of fluid (n = 1). Clinical edema resolved after 2 to 48 hours, and patients were discharged 1 to 20 days postoperatively. Serious complications included transfer to the intensive care unit (n = 14), anterior interosseous nerve palsy (n = 4), rhabdomyolysis (n = 1), and death (n = 1). Conclusion: Fluid extravasation has the potential to be a life-threatening complication of shoulder arthroscopic surgery; however, it is most commonly managed nonoperatively, and symptoms typically resolve with no evidence of long-term complications. Intraoperative surgical decisions, such as minimizing the surgical time and volume of irrigation fluid used, may limit fluid extravasation, while careful intraoperative monitoring may facilitate prompt diagnosis and management to optimize patient outcomes.
Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia

Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).
T Cell Receptor Alpha Chain Genes in the Teleost Ballan Wrasse (Labrus bergylta) Are Subjected to Somatic Hypermutation

Previously, somatic hypermutation (SHM) was considered to be exclusively associated with affinity maturation of antibodies, although it also occurred in T cells under certain conditions. More recently, it has been shown that SHM generates diversity in the variable domain of T cell receptor (TCR) in camel and shark. Here, we report somatic mutations in TCR alpha chain genes of the teleost fish, Ballan wrasse (Labrus bergylta), and show that this mechanism adds extra diversity to the polymorphic constant (C) region as well. The organization of the TCR alpha/delta locus in Ballan wrasse was obtained from a scaffold covering a single copy C alpha gene, 65 putative J alpha segments, a single copy C delta gene, 1 J delta segment, and 2 D delta segments. Analysis of 37 fish revealed 6 allotypes of the C alpha gene, each with 1–3 replacement substitutions. Somatic mutations were analyzed by molecular cloning of TCR alpha chain cDNA. Initially, 79 unique clones comprising four families of variable (V) alpha genes were characterized. Subsequently, a more restricted PCR was performed to focus on a specific V gene. Comparison of 48 clones indicated that the frequency of somatic mutations in the VJ region was 4.5/1,000 base pairs (bps), and most prevalent in complementary determining region 2 (CDR2). In total, 45 different J segments were identified among the 127 cDNA clones, counting for most of the CDR3 diversity. The number of mutations in the C alpha chain gene was 1.76 mutations/1,000 bps and A nucleotides were most frequently targeted, in contrast to the VJ region, where G nucleotides appeared to be mutational hotspots. The replacement/synonymous ratios in the VJ and C regions were 2.5 and 1.85, respectively. Only 7% of the mutations were found to be linked to the activation-induced cytidine deaminase hotspot motif (RGYW/WRCY).
NOX Inhibition Improves β-Adrenergic Stimulated Contractility and Intracellular Calcium Handling in the Aged Rat Heart

Cardiac aging is characterized by alterations in contractility and intracellular calcium ([Ca2+]i) homeostasis. It has been suggested that oxidative stress may be involved in this process. We and others have reported that in cardiomyopathies the NADPH oxidase (NOX)-derived superoxide is increased, with a negative impact on [Ca2+]i and contractility. We tested the hypothesis that in the aged heart, [Ca2+]i handling and contractility are disturbed by NOX-derived superoxide. For this we used adults (≈5 month-old) and aged (20–24 month-old) rats. Contractility was evaluated in isolated hearts, challenged with isoproterenol. To assess [Ca2+]i, isolated cardiac myocytes were field-stimulated and [Ca2+]i was monitored with fura-2. Cardiac concentration-response to isoproterenol was depressed in aged compared to adults hearts (p < 0.005), but was restored by NOX inhibitors apocynin and VAS2870. In isolated cardiomyocytes, apocynin increased the amplitude of [Ca2+]i in aged myocytes (p < 0.05). Time-50 [Ca2+]i decay was increased in aged myocytes (p < 0.05) and reduced towards normal by NOX inhibition. In addition, we found that myofilaments Ca2+ sensitivity was reduced in aged myocytes (p < 0.05), and was further reduced by apocynin. NOX2 expression along with NADPH oxidase activity was increased in aged hearts. Phospholamban phosphorylation (Ser16/Thr17) after isoproterenol treatment was reduced in aged hearts compared to adults and was restored by apocynin treatment (p < 0.05). In conclusion, β-adrenergic-induced contractility was depressed in aged hearts, and NOX inhibition restored back to normal. Moreover, altered Ca2+ handling in aged myocytes was also improved by NOX inhibition. These results suggest a NOX-dependent effect in aged myocytes at the level of Ca2+ handling proteins and myofilaments.
Neural Network Compression using Transform Coding and Clustering

With the deployment of neural networks on mobile devices and the necessity of transmitting neural networks over limited or expensive channels, the file size of the trained model was identified as bottleneck. In this paper, we propose a codec for the compression of neural networks which is based on transform coding for convolutional and dense layers and on clustering for biases and normalizations. By using this codec, we achieve average compression factors between 7.9-9.3 while the accuracy of the compressed networks for image classification decreases only by 1%-2%, respectively.
Estrus Synchronization and Artificial Insemination with Fresh and Chilled Semen in Assaf Ewes

This paper aims to study the efficiency of two short-term progestagen (FGA vs. MAP) + eCG treatments in estrus synchronization and artificial insemination (AI) with fresh or chilled semen in Assaf ewes fertility rate. All ewes received a subcutaneous implant of exogenous melatonin 45 days before been treated with short-term progestagens + eCG. By June 1st, ewes were divided in two groups: half was treated with an intravaginal sponge impregnated with 20 mg of FGA and the other half with an intravaginal sponge impregnated with 60 mg of MAP. Progestagen treatments lasted for 6 days. At sponge withdraw, all ewes were injected with 750 IU of eCG. Ovarian activity was assessed by plasmatic progesterone levels before and after progestagens + eCG treatment. Semen was collected by electro ejaculation and extended with Andromed® or OviXcell®. AI was performed 55 hours after eCG administration with fresh or chilled semen. During AI several factors were assessed: vagina mucosa color and lubrication, external cervical Os type, cervical mucous viscosity, semen deposition place and seminal cervix outflow. Semen was deposited as deep as possible without distress or trauma cervix mucosa. All Assaf ewes presented cyclic activity before progestagen + eCG treatments (2nd fortnight of May). Short-term progestagen + eCG treatments were equally efficient (100.0%). About 76.5% of Assaf ewes were pregnant 41 days after AI. Fertility rate was influenced by external Os type, semen deposition place and seminal cervix outflow. However, this rate was not conditioned by vaginal color or lubrication, cervical mucus viscosity, semen preservation technic and semen extender.
Combining Advanced Methods in Japanese-Vietnamese Neural Machine Translation

Neural machine translation (NMT) systems have recently obtained state-of-the-art in many machine translation systems between popular language pairs because of the availability of data. For low-resourced language pairs, there are few researches in this field due to the lack of bilingual data. In this paper, we attempt to build the first NMT systems for a low-resourced language pair: Japanese-Vietnamese. We have also shown significant improvements when combining advanced methods to reduce the adverse impacts of data sparsity and improve the quality of NMT systems. In addition, we proposed a variant of Byte-Pair Encoding algorithm to perform effective word segmentation for Vietnamese texts and alleviate the rare-word problem that persists in NMT systems.
Deep Di erential Recurrent Neural Networks

Due to the special gating schemes of Long Short-Term Memory (LSTM), LSTMs have shown greater potential to process complex sequential information than the traditional Recurrent Neural Network (RNN). e conventional LSTM, however, fails to take into consideration the impact of salient spatio-temporal dynamics present in the sequential input data. is problem was rst addressed by the dierential Recurrent Neural Network (dRNN), which uses a dierential gating scheme known as Derivative of States (DoS). DoS uses higher orders of internal state derivatives to analyze the change in information gain caused by the salient motions between the successive frames. e weighted combination of several orders of DoS is then used to modulate the gates in dRNN. While each individual order of DoS is good at modeling a certain level of salient spatio-temporal sequences, the sum of all the orders of DoS could distort the detected motion paerns. To address this problem, we propose to control the LSTM gates via individual orders of DoS and stack multiple levels of LSTM cells in an increasing order of state derivatives. e proposed model progressively builds up the ability of the LSTM gates to detect salient dynamical paerns in deeper stacked layers modeling higher orders of DoS, and thus the proposed LSTM model is termed deep dierential Recurrent Neural Network (d2RNN). e eectiveness of the proposed model is demonstrated on two publicly available human activity datasets: NUS-HGA and Violent-Flows. e proposed model outperforms both LSTM and non-LSTM based state-of-the-art algorithms.
Thoracoscopic segmentectomy: hybrid approach for clinical stage I non-small cell lung cancer.

Background Recently, minimally invasive surgical approaches have been developed, typified by video-assisted thoracic surgery (VATS). A meticulous surgical procedure to prevent local recurrence is required during segmentectomy for clinical stage I non-small-cell primary lung cancer. In this article, we demonstrated the validity of hybrid VATS segmentectomy. Methods Of these 125 patients, 62 (49.6%) underwent intensively radical segmentectomy (RS). The remaining 63 (50.4%) patients underwent palliative segmentectomy (PS). We used two 2-cm ports and performed a muscle-sparing mini-thoracotomy in which a partially open metal retractor allowed direct, thoracoscopic visualization as hybrid VATS segmentectomy in 63.2% of our cases. Results The consolidation/tumor ratio obtained with thin-sliced computed tomography was significantly lower in RS cases than in PS cases (P=0.001). The proportion of pathological stage IA cases was significantly higher in RS cases (95.2%) than in PS cases (66.7%; P<0.01). Five-year overall survival (OS) for clinical stage I was 100.0% in RS cases and 73.5% in PS cases (log-rank P<0.001). Five-year disease-free survival (DFS) was 95.5% and 55.7%, respectively (log-rank P<0.001). Conclusions During segmentectomy, the most critical consideration is establishment of sufficient surgical margins around the cancer. Our hybrid approach that includes meticulous surgical manipulations may produce sufficient surgical margins.
Characterization of Copy Number Variations in the Human Genome

(Slagboom et al., 1994), as well as both the replicative history of the cell lineage and environmental factors such as exposure to stress and oxidative damage (Wright and Shay, 2002; Aviv et al., 2003; Epel et al., 2004). A single-stranded, G-rich overhang produced as a result of the RNA priming requirement for DNA replication or by post-replicative processing steps (Sfeir et al., 2005) is involved in the formation of a t-loop secondary structure (Griffith et al., 1999) believed to be required for proper telomere function. Disruption of t-loop or associated telomeric chromatin structures by interference with Shelterin protein components required for their formation and maintenance (Karlseder et al., 2002), by loss of the G-overhang itself, or by a critically short tract of (TTAGGG)n can each lead to telomere dysfunction (de Lange, 2005). Depending on the cellular context (especially the presence or absence of a functional p53 pathway), such telomere loss or uncapping can trigger cellular senescence, apoptosis, and/or genome instability. The replicative capacity of cells is limited by telomere length, implicating short telomere length in age-related diseases (Harley et al., 1990; Lee et al., 1998). Supporting this Abstract. Copy number variation is a defining characteristic of human subtelomeres. Human subtelomeric segmental duplication regions (‘Subtelomeric Repeats’) comprise about 25% of the most distal 500 kb and 80% of the most distal 100 kb in human DNA. Huge allelic disparities seen in subtelomeric DNA sequence content and organization are postulated to have an impact on the dosage of transcripts embedded within the duplicated sequences, on the transcription of genes in adjacent single copy DNA regions, and on the chromatin structures mediating telomere functions including chromosome stability. In addition to the complex duplicon substructure and huge allelic variations in extended subtelomere regions, both copy number variation and alternative sequence organizations for DNA char-
Generalized Pattern Matching Micro-Engine

Many big data applications including dictionary-based decoding, deep packet inspection, Bioinformatics (DNA Alignment), and JSON/XML processing depend on fast pattern matching – well-known as difficult to accelerate. We have designed a novel heterogeneous architecture, called the Generalized Pattern Matching micro-engine (GenPM), to accelerate FSM-based applications. GenPM balances programmability and performance, employing a novel micro-architecture and software interface. We implement and evaluate GenPM in a 32nm TSMC process using a Snort network monitoring workload. Results show 64-way, 16-step GenPM can reduce instruction count by >1800x, effectively eliminating instruction management as a bottleneck. Remarkably, this reduction produces >2400x performance increase and energy efficiency benefits of 980x. Less aggressive GenPM’s, such as 8-way,16-step achieve 200-fold instruction reduction, 300-fold performance increase, and 170-fold energy efficiency benefit. GenPM approaches ASIC efficiency, while maintaining programmability.