nils-herrmann/clean_scirepeval huggingface dataset:
Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis.

Persistent mucosal inflammation and microbial infection are characteristics of chronic rhinosinusitis (CRS). Mucosal microbiota dysbiosis is found in other chronic inflammatory diseases; however, the relationship between sinus microbiota composition and CRS is unknown. Using comparative microbiome profiling of a cohort of CRS patients and healthy subjects, we demonstrate that the sinus microbiota of CRS patients exhibits significantly reduced bacterial diversity compared with that of healthy controls. In our cohort of CRS patients, multiple, phylogenetically distinct lactic acid bacteria were depleted concomitant with an increase in the relative abundance of a single species, Corynebacterium tuberculostearicum. We recapitulated the conditions observed in our human cohort in a murine model and confirmed the pathogenic potential of C. tuberculostearicum and the critical necessity for a replete mucosal microbiota to protect against this species. Moreover, Lactobacillus sakei, which was identified from our comparative microbiome analyses as a potentially protective species, defended against C. tuberculostearicum sinus infection, even in the context of a depleted sinus bacterial community. These studies demonstrate that sinus mucosal health is highly dependent on the composition of the resident microbiota as well as identify both a new sino-pathogen and a strong bacterial candidate for therapeutic intervention.
Compiler Transformations for High-Performance Computing

In the last three decades a large number of compiler transformations for optimizing programs have been implemented. Most optimizations for uniprocessors reduce the number of instructions executed by the program using transformations based on the analysis of scalar quantities and data-flow techniques. In contrast, optimizations for high-performance superscalar, vector, and parallel processors maximize parallelism and memory locality with transformations that rely on tracking the properties of arrays using loop dependence analysis.
This survey is a comprehensive overview of the important high-level program restructuring techniques for imperative languages, such as C and Fortran. Transformations for both sequential and various types of parallel architectures are covered in depth. We describe the purpose of each transformation, explain how to determine if it is legal, and give an example of its application.
Programmers wishing to enhance the performance of their code can use this survey to improve their understanding of the optimizations that compilers can perform, or as a reference for techniques to be applied manually. Students can obtain an overview of optimizing compiler technology. Compiler writers can use this survey as a reference for most of the important optimizations developed to date, and as bibliographic reference for the details of each optimization. Readers are expected to be familiar with modern computer architecture and basic program compilation techniques.
Indirect comparison of randomised controlled trials: comparative efficacy of dexlansoprazole vs. esomeprazole in the treatment of gastro-oesophageal reflux disease.

Dexlansoprazole is a new proton pump inhibitor (PPI) with a dual delayed-release system. Both dexlansoprazole and esomeprazole are an enantiomer of lansoprazole and omeprazole respectively. However, there is no head-to-head trial data or indirect comparison analyses between dexlansoprazole and esomeprazole.



To compare the efficacy of dexlansoprazole with esomeprazole in healing erosive oesophagitis (EO), the maintenance of healed EO and the treatment of non-erosive reflux disease (NERD).



Randomised Controlled Trials (RCTs) comparing dexlansoprazole or esomeprazole with either placebo or another PPI were systematically reviewed. Random-effect meta-analyses and adjusted indirect comparisons were conducted to compare the treatment effect of dexlansoprazole and esomeprazole using a common comparator. The relative risk (RR) and 95% confidence interval (CI) were calculated.



The indirect comparisons revealed significant differences in symptom control of heartburn in patients with NERD at 4 weeks. Dexlansoprazole 30 mg was more effective than esomeprazole 20 mg or 40 mg (RR: 2.01, 95% CI: 1.15-3.51; RR: 2.17, 95% CI: 1.39-3.38). However, there were no statistically significant differences between the two drugs in EO healing and maintenance of healed EO. Comparison of symptom control in healed EO was not able to be made due to different definitions used in the RCTs.



Adjusted indirect comparisons based on currently available RCT data suggested significantly better treatment effect in symptom control of heartburn in patients with NERD for dexlansoprazole against esomeprazole. No statistically significant differences were found in other EO outcomes. However, these study findings need to be interpreted with caution due to small number of studies and other limitations.
Randomized controlled trial of specific spinal stabilization exercises and conventional physiotherapy for recurrent low back pain.

Pragmatic, multicentered randomized controlled trial, with 12-month follow-up.



To evaluate the effect of adding specific spinal stabilization exercises to conventional physiotherapy for patients with recurrent low back pain (LBP) in the United Kingdom.



Spinal stabilization exercises are a popular form of physiotherapy management for LBP, and previous small-scale studies on specific LBP subgroups have identified improvement in outcomes as a result.



A total of 97 patients (18-60 years old) with recurrent LBP were recruited. Stratified randomization was undertaken into 2 groups: "conventional," physiotherapy consisting of general active exercise and manual therapy; and conventional physiotherapy plus specific spinal stabilization exercises. Stratifying variables used were laterality of symptoms, duration of symptoms, and Roland Morris Disability Questionnaire score at baseline. Both groups received The Back Book, by Roland et al. Back-specific functional disability (Roland Morris Disability Questionnaire) at 12 months was the primary outcome. Pain, quality of life, and psychologic measures were also collected at 6 and 12 months. Analysis was by intention to treat.



A total of 68 patients (70%) provided 12-month follow-up data. Both groups showed improved physical functioning, reduced pain intensity, and an improvement in the physical component of quality of life. Mean change in physical functioning, measured by the Roland Morris Disability Questionnaire, was -5.1 (95% confidence interval -6.3 to -3.9) for the specific spinal stabilization exercises group and -5.4 (95% confidence interval -6.5 to -4.2) for the conventional physiotherapy group. No statistically significant differences between the 2 groups were shown for any of the outcomes measured, at any time.



Patients with LBP had improvement with both treatment packages to a similar degree. There was no additional benefit of adding specific spinal stabilization exercises to a conventional physiotherapy package for patients with recurrent LBP.
Brain Tumor Classification Using Wavelet and Texture Based Neural Network

Brain tumor is one of the major causes of death among people. It is evident that the chances of survival can be increased if the tumor is detected and classified correctly at its early stage. Conventional methods involve invasive techniques such as biopsy, lumbar puncture and spinal tap method, to detect and classify brain tumors into benign (non cancerous) and malignant (cancerous). A computer aided diagnosis algorithm has been designed so as to increase the accuracy of brain tumor detection and classification, and thereby replace conventional invasive and time consuming techniques. This paper introduces an efficient method of brain tumor classification, where, the real Magnetic Resonance (MR) images are classified into normal, non cancerous (benign) brain tumor and cancerous (malignant) brain tumor. The proposed method follows three steps, (1) wavelet decomposition, (2) textural feature extraction and (3) classification. Discrete Wavelet Transform is first employed using Daubechies wavelet (db4), for decomposing the MR image into different levels of approximate and detailed coefficients and then the gray level co-occurrence matrix is formed, from which the texture statistics such as energy, contrast, correlation, homogeneity and entropy are obtained. The results of co-occurrence matrices are then fed into a probabilistic neural network for further classification and tumor detection. The proposed method has been applied on real MR images, and the accuracy of classification using probabilistic neural network is found to be nearly 100%.
Cyber-physical systems: Milestones and research challenges

In the past decade, we have witnessed an unparalleled success of information and communication technologies (ICT), which is expected to be even more proliferating and ubiquitous in the future. Among many ICT applications, ICT components embedded into various devices and systems have become a critical one. In fact, embedded systems with communication capability span virtually every aspect of our daily life. An embedded system is defined as a computer system designed to perform dedicated specific functions, usually under real-time computing constraints. It is called ‘‘embedded’’ because it is embedded as a part of a complete device or system. By contrast, a general-purpose computer is designed to satisfy a wide range of user requirements. Embedded systems range from portable devices such as smart phones and MP3 players, to large installations like plant control systems. Recently, the convergence of cyber and physical spaces  has further transformed traditional embedded systems into cyberphysical systems (CPS), which are characterized by tight integration and coordination between computation and physical processes by means of networking. In CPS, various embedded devices with computational components are networked to monitor, sense, and actuate physical elements in the real world. Examples of CPS encompass a wide range of large-scale engineered systems such as avionics, healthcare, transportation, automation, and smart grid systems. In addition, the recent proliferation of smart phones and mobile Internet devices equipped with multiple sensors can be leveraged to enable mobile cyber-physical applications. In all of these systems, it is of critical importance to properly resolve the complex interactions between various computational and physical elements. In this guest editorial, we first provide an overview of CPS by introducing major issues in CPS as well as recent research efforts and future opportunities for CPS. Then, we summarize the papers in the special section by clearly describing their main contributions on CPS research. The remainder of the editorial is organized as follows: In Section 2, we provide an overview of CPS. We first explain the key characteristics of CPS compared to the traditional embedded systems. Then, we introduce the recent trend in CPS research with an emphasis on major research topics in CPS. We introduce recent CPS-related projects in Section 3. Summary of the papers in the special section follows in Section 4 by focusing on their contributions on CPS research. Finally, our conclusion follows in Section 5.
The thermodynamics of DNA structural motifs.

DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
Air-core transformer integration for GaN VHF converters

This paper proposes an air-core transformer integration method, which mounts the transformer straightly into the multi-layer PCB, and maintains the proper distance between the inner transformer and other components on the top layer. Compared with other 3D integration method, the air-core transformer is optimized and modeled carefully to avoid the electromagnetic interference (EMI) of the magnetic fields. The integration method reduces the PCB area significantly, ensuring higher power density and similar efficiency as the conventional planar layout because the air-core transformer magnetic field does not affect other components. Moreover, the converters with the integrated PCB transformer can be manufactured with high consistency. With the air-core transformer, the overall height is only the sum of twice the PCB thickness and components height. In addition, the proposed integration method reduces the power loop inductance by 64%. It is applied to two resonant flyback converters operating at 20 MHz with Si MOSFETs, and 30 MHz with eGaN HEMTs respectively. The full load efficiency of the 30 MHz prototype is 80.1% with 5 V input and 5 V/ 2 W output. It achieves the power density of 32 W/in3.
Neurological impressions on the organization of language networks in the human brain.

More than 95% of right-handed individuals, as well as almost 80% of left-handed individuals, have left hemisphere dominance for language. The perisylvian networks of the dominant hemisphere tend to be the most important language systems in human brains, usually connected by bidirectional fibres originated from the superior longitudinal fascicle/arcuate fascicle system and potentially modifiable by learning. Neuroplasticity mechanisms take place to preserve neural functions after brain injuries. Language is dependent on a hierarchical interlinkage of serial and parallel processing areas in distinct brain regions considered to be elementary processing units. Whereas aphasic syndromes typically result from injuries to the dominant hemisphere, the extent of the distribution of language functions seems to be variable for each individual.



Review of the literature  Several theories try to explain the organization of language networks in the human brain from a point of view that involves either modular or distributed processing or sometimes both. The most important evidence for each approach is discussed under the light of modern theories of organization of neural networks.



Understanding the connectivity patterns of language networks may provide deeper insights into language functions, supporting evidence-based rehabilitation strategies that focus on the enhancement of language organization for patients with aphasic syndromes.
The Change of Stretched Penile Length and Anthropometric Data in Korean Children Aged 0–14 Years: Comparative Study of Last 25 Years

There has been a great improvement in height and weight of Korean children owing to economic development over the last 25 years. This study aimed to evaluate the penile length of Korean children today and to compare it with a previous Korean study reported in 1987. The cross-sectional study was conducted with 909 Korean boys aged 0-14 years who had been brought to outpatient clinics of five tertiary hospitals (Busan, Ulsan, and Changwon) between September 2013 and May 2015. The stretched penile length (SPL) was measured and the testicular size was measured using orchidometry (mL). Student's t-test or Mann-Whitney U test was used to compare the result of our study and the study reported in 1987. SPL of Korean children gradually increased from 4.1 ± 0.8 cm at 0-1 year old to 9.6 ± 3.0 cm at 13-14 years old, the most rapidly during the age of 13. While body weight and testicular size significantly increased from 1987 in most of age groups, there were no significant changes in SPL although there was in some age groups. Height decreased in the infants < 1 year old and increased in the children > 6 years old. With the great economic development over the last quarter century in Korea, height, body weight, and testicular size of children significantly increased but there was no significant change in SPL except penile growth pattern.
Isolation and Emotions in the Workplace: The Influence of Perceived Media Richness and Virtuality

Remote work and intensive use of Information Technologies (IT) are increasingly common in organizations. At the same time, professional stress seems to develop. However, IS research has paid little attention to the relationships between these two phenomena. The purpose of this research in progress is to present a framework that introduces the influence of (1) new spatial and temporal constraints and of (2) intensive use of IT on employee emotions at work. Specifically, this paper relies on virtuality (e.g. Chudoba et al. 2005) and media richness (Daft and Lengel 1984) theories to determine the emotional consequences of geographically distributed work.
Shared Binary Decision Diagram with Attributed Edges for Efficient Boolean function Manipulation

The efficiency of Boolean function manipulation depends on the form of representation of Boolean functions. Binary Decision Diagrams (BDD's) are graph representations proposed by Akers and Bryant. BDD's have some properties which can be used to enable efficient Boolean function manipulation.
In this paper, we describe a technique of more efficient Boolean function manipulation that uses Shared Binary Decision Diagrams (SBDD's) with attributed edges. Our implements include an ordering algorithm of input variables and a method of handling don't care. We show experimental results produced by the implementation of the Boolean function manipulator.
Post-surgical wound management of pilonidal cysts with a haemoglobin spray: a case series.

Painful acute cysts in the natal cleft or lower back, known as pilonidal sinus disease, are a severe burden to many younger patients. Although surgical intervention is the preferred first line treatment, postsurgical wound healing disturbances are frequently reported due to infection or other complications. Different treatment options of pilonidal cysts have been discussed in the literature, however, no standardised guideline for the postsurgical wound treatment is available. After surgery, a common recommended treatment to patients is rinsing the wound with clean water and dressing with a sterile compress. We present a case series of seven patients with wounds healing by secondary intention after surgical intervention of a pilonidal cyst. The average age of the patients was 40 years old. Of the seven patients, three had developed a wound healing disturbance, one wound had started to develop a fibrin coating and three were in a good condition. The applied wound care regimens comprised appropriate mechanical or autolytic debridement, rinsing with an antimicrobial solution, haemoglobin application, and primary and secondary dressings. In all seven cases a complete wound closure was achieved within an average of 76 days with six out of seven wounds achieving wound closure within 23-98 days. Aesthetic appearance was deemed excellent in five out of seven cases excellent and acceptable in one. Treatment of one case with a sustained healing disturbance did result in wound closure but with a poor aesthetic outcome and an extensive cicatrisation of the new tissue. Based on these results we recommend that to avoid healing disturbances of wounds healing by secondary intention after surgical pilonidal cyst intervention, an adequate wound care regime comprising appropriate wound debridement, rinsing, topically applied haemoglobin and adequate wound dressing is recommendable as early as possible after surgery.
Chromosomal-array analysis reveals partial 11q duplication and partial 12p deletion in a mildly affected case.

Partial trisomy 11q is a rare syndrome and may be observed due to an intra-chromosomal duplication or an inter-chromosomal insertion. The deletions of the short arm of chromosome 12 are also uncommon structural aberrations. Only a small fraction of structural chromosome anomalies are related to the unbalanced progeny of balanced translocation carrier parents. We here report on a 10-month-old baby boy who shows a very mild phenotype related to unique chromosomal abnormality, partial trisomy of 11q, and partial monosomy of 12p, due to the maternal balanced reciprocal translocation (11;12). The proband showed a 49.64 Mb duplication of 11q14.1-q25 and 0.44 Mb deletion of 12p13.33 in chromosomal array analysis. Since it is known that the duplications may cause a milder phenotype than deletions. Dysmorphic facial features, minor cardiac anomalies, respiratory distress, central nervous system anomalies, and psychomotor delay observed in the patient was similar to the reported pure 11q duplication cases, while behavioral problems observed in pure monosomy 12p cases could not be evaluated due to the young age of the patient. Phenotype-genotype correlation will be discussed in view of all the reported pure partial 11q trisomies and pure partial 12p deletion cases.
On the Safety of Machine Learning: Cyber-Physical Systems, Decision Sciences, and Data Products

Machine learning algorithms increasingly influence our decisions and interact with us in all parts of our daily lives. Therefore, just as we consider the safety of power plants, highways, and a variety of other engineered socio-technical systems, we must also take into account the safety of systems involving machine learning. Heretofore, the definition of safety has not been formalized in a machine learning context. In this article, we do so by defining machine learning safety in terms of risk, epistemic uncertainty, and the harm incurred by unwanted outcomes. We then use this definition to examine safety in all sorts of applications in cyber-physical systems, decision sciences, and data products. We find that the foundational principle of modern statistical machine learning, empirical risk minimization, is not always a sufficient objective. We discuss how four different categories of strategies for achieving safety in engineering, including inherently safe design, safety reserves, safe fail, and procedural safeguards can be mapped to a machine learning context. We then discuss example techniques that can be adopted in each category, such as considering interpretability and causality of predictive models, objective functions beyond expected prediction accuracy, human involvement for labeling difficult or rare examples, and user experience design of software and open data.