Miracle-dz/UniFAR-FTUs huggingface dataset:
A Preliminary Investigation of Laparoscopic Fundoplication Treatment on Gastroesophageal Reflux Disease-related Respiratory Symptoms

Background: Extraesophageal syndromes are more difficult to identify and treat than the usual esophageal symptoms. The current study explores the efficacy of laparoscopic Nissen fundoplication (LNF) on gastroesophageal reflux disease (GERD)-related respiratory symptoms (RSs) during a 12-month follow-up observation. Methods: From April 2008 to September 2009, LNF was performed on 198 patients (107 men and 91 women) with GERD-related RSs according to underlying esophageal motility. A questionnaire form ranging from 0 to 5 was the basic requirement for recording pretreatment and posttreatment and for making detailed evaluation of the symptoms. All scores of GERD-related RSs, such as heartburn, regurgitation, coughing, breathe holding, wheezing, shortness of breath, and choking, significantly decreased at the 12th month. Results: All the patients who participated in the current study were adults and elders aged 22 to 84 years with a mean age of 49±12.89. The median length of stay was 4.3 days with a range of 2 to 8 days. The median score of heartburn, regurgitation, coughing, wheezing, shortness of breath, choking, and chest pain decreased from 4.92±1.99, 4.98±1.81, 7.23±1.87, 7.50±1.88, 5.83±2.13, 5.94±2.22, and 4.92±1.88 to 1.62±2.33, 0.64±1.43, 2.79±2.82, 2.53±2.96, 1.37±2.10, 1.28±2.09, and 1.57±2.55 (P<0.01), respectively. A total of 173 patients had various relieved symptom scores, 16 patients (8.1%) had different scale recurrence of symptoms after laparoscopic fundoplication treatment, and 13 patients had to retreat to omeprazole as an auxiliary medical therapy. Three other patients rejected any therapy, and no deaths occurred. A single patient converted from laparoscopic surgery to open surgery. Several short-term symptoms included retrosternal uneasiness or pain (n=63; 31.8%), dysphagia (n=45; 22.7%), abdominal distension (n=87; 43.9%), and diarrhea (n=23; 11.6%). Early dysphagia lasting <6 weeks was common, and 45 patients (22.7%) underwent an early esophagogastroduodenoscopy or contrast swallow. Five patients (2.5%) who had prolonged dysphagia during the 6-month clinical review required esophageal dilatation, and the outcomes were successful. Conclusions: LNF can be an effective means for treating RSs in patients with GERD.
An optimal subgradient algorithm for large-scale convex optimization in simple domains

This paper shows that the optimal subgradient algorithm, OSGA, proposed in \cite{NeuO} can be used for solving structured large-scale convex constrained optimization problems. Only first-order information is required, and the optimal complexity bounds for both smooth and nonsmooth problems are attained. More specifically, we consider two classes of problems: (i) a convex objective with a simple closed convex domain, where the orthogonal projection on this feasible domain is efficiently available; (ii) a convex objective with a simple convex functional constraint. If we equip OSGA with an appropriate prox-function, the OSGA subproblem can be solved either in a closed form or by a simple iterative scheme, which is especially important for large-scale problems. We report numerical results for some applications to show the efficiency of the proposed scheme. A software package implementing OSGA for above domains is available.
Nonconvex Compressed Sensing by Nature-Inspired Optimization Algorithms

The l0 regularized problem in compressed sensing reconstruction is nonconvex with NP-hard computational complexity. Methods available for such problems fall into one of two types: greedy pursuit methods and thresholding methods, which are characterized by suboptimal fast search strategies. Nature-inspired algorithms for combinatorial optimization are famous for their efficient global search strategies and superior performance for nonconvex and nonlinear problems. In this paper, we study and propose nonconvex compressed sensing for natural images by nature-inspired optimization algorithms. We get measurements by the block-based compressed sampling and introduce an over-complete dictionary of Ridgelet for image blocks. An atom of this dictionary is identified by the parameters of direction, scale and shift. Of them, direction parameter is important for adapting to directional regularity. So we propose a two-stage reconstruction scheme (TS_RS) of nature-inspired optimization algorithms. In the first reconstruction stage, we design a genetic algorithm for a class of image blocks to acquire the estimation of atomic combinations in all directions; and in the second reconstruction stage, we adopt clonal selection algorithm to search better atomic combinations in the sub-dictionary resulted by the first stage for each image block further on scale and shift parameters. In TS_RS, to reduce the uncertainty and instability of the reconstruction problems, we adopt novel and flexible heuristic searching strategies, which include delicately designing the initialization, operators, evaluating methods, and so on. The experimental results show the efficiency and stability of the proposed TS_RS of nature-inspired algorithms, which outperforms classic greedy and thresholding methods.
Large scale, high density integration of all spin logic

Spintronics brings new features that make it a viable candidate technology to implement non-conventional processing for new computing paradigms in an efficient way. The first milestone of the spintronics roadmap was the fabrication of hybrid systems where the data processing relies mostly on charge-based electronics devices (CMOS), while the memory hierarchy is partially or totally replaced by MRAM. In the next step, spintronics can also be used for data processing, still in conjunction with CMOS. Nevertheless, replacing all the processing by pure spintronic circuits, without any charge current, remains the ultimate objective of spintronics. All spin logic (ASL) paves the way towards that goal, even if some CMOS control circuits are still necessary. However, as ASL does not rely on the same computing principle as CMOS, it is necessary to address some specific issues. Pure spin current propagates in every direction, including backwards in the presence of multiple inputs; and is divided when crossings are encountered. It combines mainly linearly, while logic operations require non-linear binary decisions. Interconnect between logic gates requires directionality from inputs to outputs, and fanout with negligible signal attenuation. In this context, we develop new strategies for ASL modeling and logic design. We propose an architecture and a design strategy based on a high-density array to address the specific issues of directionality, attenuation and linearity. Moreover, the feasibility is supported through the modeling and the simulation of its basic block. This implies modularity to simulate complex circuits, even when they are ahead of today's experimental demonstrations.
Early, progressive, and sustained dysfunction of sensory axons underlies paclitaxel‐induced neuropathy

Paclitaxel is used in the adjuvant treatment of breast cancer. It induces disabling and potentially long‐lasting sensory neuropathy. This study systematically and prospectively investigated sensory function, using clinical grading scales, quantitative sensory testing, and neurophysiological and nerve excitability studies in 28 patients with early‐stage breast cancer. After administration of 529 ± 41 mg/m2 paclitaxel, 71% of patients developed neuropathic symptoms by 6 weeks of treatment. Early and progressive increases in stimulus threshold (P < 0.05) and reduction in sensory amplitudes from 47.0 ± 3.3 μV to 42.4 ± 3.4 μV (P < 0.05) occurred by 4 weeks, with a further reduction by final treatment (33.7 ± 3.0 μV, P < 0.001). The majority of patients (63%) did not experience recovery of neuropathic symptoms at follow‐up. Axonal disruption did not relate to membrane conductance dysfunction. We found that paclitaxel produces early sensory dysfunction and leads to persistent neuropathy. Importantly, significant axonal dysfunction within the first month of treatment predated symptom onset, suggesting a window for neuroprotective therapies. Muscle Nerve, 2011
Extracting old persian cuneiform font out of noisy images (handwritten or inscription)

The process of converting the text in the digital image to font (encrypted text) is called OCR. This paper is involved with extracting inscribed texts on the Achaemenid inscriptions. This is the first proper quality example of using OCR to recognizing Achaemenid scripts. There are different approaches to recognizing characters, of which we have chosen open source Tesseract engine for segmentation, learning and classification in this research. Due to existence of noise (stone crack) in inscriptions, this paper uses some image processing techniques to eliminate noises. This system's final output includes: extraction of cuneiform font, Persian and English transcription of sentences, sentence pronunciation and translation of a substantial number of extracted Persian and English words, which makes us better understand the way they spoke in that era. Acquired results of validation and result section indicates that this system has been able to properly cope with the recognition of cuneiform characters and has classified all characters of test data properly with about 92% accuracy. The acquired results are promising that they are able to make and improve NLP in this area.
Historical Perspectives and Guidelines for Botulinum Neurotoxin Subtype Nomenclature

Botulinum neurotoxins are diverse proteins. They are currently represented by at least seven serotypes and more than 40 subtypes. New clostridial strains that produce novel neurotoxin variants are being identified with increasing frequency, which presents challenges when organizing the nomenclature surrounding these neurotoxins. Worldwide, researchers are faced with the possibility that toxins having identical sequences may be given different designations or novel toxins having unique sequences may be given the same designations on publication. In order to minimize these problems, an ad hoc committee consisting of over 20 researchers in the field of botulinum neurotoxin research was convened to discuss the clarification of the issues involved in botulinum neurotoxin nomenclature. This publication presents a historical overview of the issues and provides guidelines for botulinum neurotoxin subtype nomenclature in the future.
The convergence of a PLL with variable parameters

A phase-locked loop with variable parameters is considered. In such a system it is possible to obtain a short convergence time together with a small bandwidth. It is supposed that the PLL's parameters cannot be switched and there is a restriction on the velocity of the parameter variation. An optimal strategy of parameter variation is obtained which gives an improvement in convergence time by a factor of about 30 in comparision to fixed parameter and small-bandwidth PLLs.
Ensembl 2017

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.
Outcomes of patients with cirrhosis and hepatorenal syndrome type 1 treated with liver transplantation

Hepatorenal syndrome type 1 (HRS1) is acute renal failure in the setting of advanced cirrhosis, and it results from hemodynamic derangements, which should be fully reversible after liver transplantation. However, the rate of hepatorenal syndrome (HRS) reversal and factors predicting renal outcomes after transplantation have not been fully elucidated. The aim of this study was to assess outcomes of HRS1 patients after liver transplantation and factors predicting HRS reversal. A chart review of all liver transplant patients with HRS1 (according to International Ascites Club criteria) at Toronto General Hospital from 2001 to 2010 was conducted. Patient demographic data, pretransplant and posttransplant laboratory data, and the presence of and time to posttransplant HRS reversal (serum creatinine < 1.5 mg/dL) were extracted from the center's transplant electronic database. Patients were followed until death or the end of the 2011 calendar year. Sixty‐two patients (mean age, 54.7 ± 1.2 years; mean Model for End‐Stage Liver Disease score, 35 ± 1) with HRS1 (serum creatinine, 3.37 ± 0.13 mg/dL) at liver transplant were enrolled. Thirty‐eight patients received midodrine, octreotide, and albumin without success and subsequently received renal dialysis. One further patient received dialysis without pharmacotherapy. After liver transplantation, HRS1 resolved in 47 of 62 patients (75.8%) at a mean time of 13 ± 2 days. Patients without HRS reversal had significantly higher pretransplant serum creatinine levels (3.81 ± 0.34 versus 3.23 ± 0.14 mg/dL, P = 0.06), a longer duration of HRS1 {25 days [95% confidence interval (CI), 16‐42 days] versus 10 days (95% CI, 10‐18 days), P = 0.02}, a longer duration of pretransplant dialysis [27 days (95% CI, 13‐41 days) versus 10 days (95% CI, 6‐14 days), P = 0.01], and increased posttransplant mortality (P = 0.0045) in comparison with those whose renal function recovered. The only predictor of HRS1 nonreversal was the duration of pretransplant dialysis with a 6% increased risk of nonreversal with each additional day of dialysis. In conclusion, our study suggests that patients with HRS1 should receive a timely liver transplant to improve their outcome. Liver Transpl 21:300–307, 2015. © 2015 AASLD.
Use of telecytology for the immediate assessment of CT guided and endoscopic FNA cytology: Diagnostic accuracy, advantages, and pitfalls

Telecytology (TC) can assist cytopathologists in efficiently providing immediate evaluation for fine needle aspirations (FNAs) performed at remote locations. Our aim was to evaluate the accuracy and feasibility of TC for immediate assessments of FNAs. Phase I: Diff‐Quik and Pap stained smears from two retrospective sets of 20 pilot cases each (n = 40) were included for TC assessments. For the first set, diagnoses were rendered by four pathologists and for the second set, in addition, four cytotechnologists also participated. Diagnostic concordance with the final diagnosis was assessed. Phase IIA: These were followed by real time assessments (RTA) of 56 TC FNAs and diagnostic concordance was compared to that of 100 conventional in‐person immediate assessments (Phase IIB).
StreamFTL: Stream-level address translation scheme for memory constrained flash storage

Although much research efforts have been devoted to reducing the size of address mapping table which consumes DRAM space in solid state drives (SSDs), most SSDs still use page-level mapping for high performance in their firmware called flash translation layer (FTL). In this paper, we propose a novel FTL scheme, called StreamFTL. In order to reduce the size of the mapping table in SSDs, StreamFTL maintains a mapping entry for each stream, which consists of several logical pages written at contiguous physical pages. Unlike extent, which is used by previous FTL schemes, the logical pages in a stream do not need to be contiguous. We show that StreamFTL can reduce the size of the mapping table by up to 90% compared to page-level mapping scheme.
The strategy of psychopathy: primary psychopathic traits predict defection on low-value relationships

Recent evidence suggests that psychopathy is a trait continuum. This has unappreciated implications for understanding the selective advantage of psychopathic traits. Although clinical psychopathy is typically construed as a strategy of unconditional defection, subclinical psychopathy may promote strategic conditional defection, broadening the adaptive niche of psychopathy within human societies. To test this, we focus on a ubiquitous real-life source of conditional behaviour: the expected relational value of social partners, both in terms of their quality and the likely quantity of future interactions with them. We allow for conversational interaction among participants prior to their playing an unannounced, one-shot prisoner's dilemma game, which fosters naturalistic interpersonal evaluation and conditional behaviour, while controlling punishment and reputation effects. Individuals scoring higher on factor 1 (callous affect, interpersonal manipulation) of the Levenson self-report psychopathy scale defected conditionally on two kinds of low-value partners: those who interrupted them more during the conversation, and those with whom they failed to discover cues to future interaction. Both interaction effects support the hypothesis that subclinical primary psychopathy potentiates defection on those with low expected relational value. These data clarify the function and form of psychopathic traits, while highlighting adaptive variation in human social strategies.
On Non-Interactive Simulation of Joint Distributions

We consider the following non-interactive simulation problem: Alice and Bob observe sequences Xn and Yn, respectively, where ((Xi, Yi)}i=1n are drawn independent identically distributed from P(x, y), and they output U and V, respectively, which is required to have a joint law that is close in total variation to a specified Q(u, v). It is known that the maximal correlation of U and V must necessarily be no bigger than that of X and Y if this is to be possible. Our main contribution is to bring hypercontractivity to bear as a tool on this problem. In particular, we show that if P(x, y) is the doubly symmetric binary source, then hypercontractivity provides stronger impossibility results than maximal correlation. Finally, we extend these tools to provide impossibility results for the k-agent version of this problem.
Finite Ground Coplanar (FGC) Waveguide: It's Characteristics and Advantages for Use in RF and Wireless Communication Circuits

To solve many of the problems encountered when using conventional coplanar waveguide (CPW) with its semiinfinite ground planes, a new version of coplanar waveguide with electrically narrow ground planes has been developed. This new transmission line which we call Finite Ground Coplanar (FGC) waveguide has several advantages which make it a better transmission line for RF and wireless circuits. Since the ground planes are electrically narrow, spurious resonances created by the CPW ground planes and the metal carrier or package base are eliminated. In addition, lumped and distributed circuit elements may now be integrated into the ground strips in the same way as they traditionally have been integrated into the center conductor to realize novel circuit layouts that are smaller and have less parasitic reactance. Lastly, FGC is shown to have lower coupling between adjacent transmission lines than conventional CPW.
The foundations of plant intelligence

Intelligence is defined for wild plants and its role in fitness identified. Intelligent behaviour exhibited by single cells and systems similarity between the interactome and connectome indicates neural systems are not necessary for intelligent capabilities. Plants sense and respond to many environmental signals that are assessed to competitively optimize acquisition of patchily distributed resources. Situations of choice engender motivational states in goal-directed plant behaviour; consequent intelligent decisions enable efficient gain of energy over expenditure. Comparison of swarm intelligence and plant behaviour indicates the origins of plant intelligence lie in complex communication and is exemplified by cambial control of branch function. Error correction in behaviours indicates both awareness and intention as does the ability to count to five. Volatile organic compounds are used as signals in numerous plant interactions. Being complex in composition and often species and individual specific, they may represent the plant language and account for self and alien recognition between individual plants. Game theory has been used to understand competitive and cooperative interactions between plants and microbes. Some unexpected cooperative behaviour between individuals and potential aliens has emerged. Behaviour profiting from experience, another simple definition of intelligence, requires both learning and memory and is indicated in the priming of herbivory, disease and abiotic stresses.
Dose–Response Models are Conditional on Determination of Causality

Causality is a key underlying issue in this special collection of articles regarding uncertainties in health risk estimates for “criteria” air pollutants in the United States and estimates of human health benefits of the National Ambient Air Quality Standards (NAAQS). Specifically, does exposure to a particular air pollutant at a particular concentration cause an adverse effect in the exposed population? However, before addressing this question, some context is required. It is not possible to discuss the risk assessment process related to the NAAQS without consideration of the legal and policy context of these standards. Therefore, some of this context is provided here. There is also a critical distinction between how information is used to inform the process of revising or setting a standard versus how it is used in benefit-cost assessment. The statutory mandate for the NAAQS is from the Clean Air Act (CAA). The CAA requires the Administrator of the U.S. Environmental Protection Agency to list those air pollutants that “cause or contribute to air pollution which may reasonably be anticipated to endanger public health or welfare. ” These pollutants are referred to as “criteria pollutants. ” Here, we will focus on NAAQS aimed at protecting public health, which are referred to as “primary” standards. The legislative and historical backgrounds for NAAQS are described in the U.S. Environmental Protection Agency’s (EPA’s) policy assessment for each of the pollutants regulated under the NAAQS. For example, see the ozone policy assessment for more details. (1) Section 109(b)(1) of the CAA directs that a primary standard allows “an adequate margin of safety” and be “requisite to protect the public health. ” This language is vague but has been interpreted as the re-