nils-herrmann/clean_scirepeval huggingface dataset:
Systematic Video-Assisted Mediastinoscopic Lymphadenectomy (VAMLA)

Accurate mediastinal lymph node dissection during thoracotomy is mandatory for staging and for adjuvant therapy in lung cancer. Pre-therapeutic staging for neoadjuvant therapy or for video assisted thoracoscopic resection of lung cancer is achieved usually by CT-scan and mediastinoscopy. However, these methods do not reach the accuracy of open nodal dissection. Therefore we developed a technique of radical video-assisted mediastinoscopic lymphadenectomy (VAMLA). This study was designed to show that VAMLA is feasible and that radicality of lymphadenectomy is comparable to the open procedure.In a prospective study all VAMLA procedures were registered and followed up in a database. Specimens of VAMLA were analysed by a single pathologist. Lymph nodes were counted and compared to open lymphadenectomy. The weight of the dissected tissue was documented. In patients receiving tumour resection subsequently to VAMLA, radicality of the previous mediastinoscopic dissection was controlled during thoracotomy.37 patients underwent video-assisted mediastinoscopy from June 1999 to April 2000. Mean duration of anaesthesia was 84.6 (SD 35.8) minutes.In 7 patients radical lymphadenectomy was not intended because of bulky nodal disease or benign disease. The remaining 30 patients underwent complete systematic nodal dissection as VAMLA.18 patients received tumour resection subsequently (12 right- and 6 left-sided thoracotomies). These thoracotomies allowed open re-dissection of 12 paratracheal regions, 10 of which were found free of lymphatic tissue. In two patients, 1 and 2 left over paratracheal nodes were counted respectively. 10/18 re-dissected subcarinal regions were found to be radically dissected by VAMLA. In 6 patients one single node and in the remaining 2 cases 5 and 8 nodes were found, respectively. However these counts also included nodes from the ipsilateral main bronchus. None of these nodes was positive for tumour.Average weight of the tissue that was harvested by VAMLA was 10.1 g (2.2-23.7, SD 6.3). An average number of 20.5 (6-60, SD 12.5) nodes per patient were counted in the specimens. This is comparable to our historical data from open lymphadenectomy.One palsy of the recurrent nerve in a patient with extensive preparation of the nerve and resection of 11 left-sided enlarged nodes was the only severe complication in this series.VAMLA seems to accomplish mediastinal nodal dissection comparable to open lymphadenectomy and supports video assisted surgery for lung cancer. In neoadjuvant setting a correct mediastinal N-staging is achieved.
Laser-Cutting Pneumatics

Pneumatic devices require tight tolerances to keep them leak-free. Specialized companies offer various off-the-shelf devices, while these work well for many applications, there are also situations where custom design and production of pneumatic parts are desired. Cost efficiency, design flexibility, rapid prototyping, and MRI compatibility requirements are reasons why we investigated a method to design and produce different pneumatic devices using a laser cutter from acrylic, acetal, and rubber-like materials. The properties of the developed valves, pneumatic cylinders, and stepper motors were investigated. At 4-bar working pressure, the 4/3-way valves are capable of 5-Hz switching frequency and provide at most 22-L/min airflow. The pneumatic cylinder delivers 48 N of force, the acrylic stepper motor 30 N. The maximum switching frequency over 6-m long transmission lines is 4.5 Hz, using 2-mm tubing. A MRI-compatible robotic biopsy system driven by the pneumatic stepper motors is also demonstrated. We have shown that it is possible to construct pneumatic devices using laser-cutting techniques. This way, plastic MRI-compatible cylinders, stepper motors, and valves can be developed. Provided that a laser-cutting machine is available, the described pneumatic devices can be fabricated within hours at relatively low cost, making it suitable for rapid prototyping applications.
Co-Selection of Resistance to Antibiotics, Biocides and Heavy Metals, and Its Relevance to Foodborne Pathogens.

Concerns have been raised in recent years regarding co-selection for antibiotic resistance among bacteria exposed to biocides used as disinfectants, antiseptics and preservatives, and to heavy metals (particularly copper and zinc) used as growth promoters and therapeutic agents for some livestock species. There is indeed experimental and observational evidence that exposure to these non-antibiotic antimicrobial agents can induce or select for bacterial adaptations that result in decreased susceptibility to one or more antibiotics. This may occur via cellular mechanisms that are protective across multiple classes of antimicrobial agents or by selection of genetic determinants for resistance to non-antibiotic agents that are linked to genes for antibiotic resistance. There may also be relevant effects of these antimicrobial agents on bacterial community structure and via non-specific mechanisms such as mobilization of genetic elements or mutagenesis. Notably, some co-selective adaptations have adverse effects on fitness in the absence of a continued selective pressure. The present review examines the evidence for the significance of these phenomena, particularly in respect of bacterial zoonotic agents that commonly occur in livestock and that may be transmitted, directly or via the food chain, to human populations.
Neuro-Ophthalmology Supranuclear control of ocular motility

Under natural circumstances, gaze shifts are accomplished by a complex combination of many individual eye movements. Such arrangement requires exquisite coordination between numerous structures involved in ocular motor control. A plethora of new evidence emanating from animal studies expanded and modified traditional schemes of premotor organization of the ocular motor system. In this article, the functional mechanisms concerned with programming eye movements are outlined, current knowledge of the relevant neuroanatomy is presented, and clinical disorders of supranuclear control of ocular motility are discussed. For further details on these topics, the reader is referred to standard texts.
Analysis of SaaS Business Platform Workloads for Sizing and Collocation

Sharing of physical infrastructure using virtualization presents an opportunity to improve the overall resource utilization. It is extremely important for a Software as a Service (SaaS) provider to understand the characteristics of the business application workload in order to size and place the virtual machine (VM) containing the application. A typical business application has a multi-tier architecture and the application workload is often predictable. Using the knowledge of the application architecture and statistical analysis of the workload, one can obtain an appropriate capacity and a good placement strategy for the corresponding VM. In this paper we propose a tool iCirrus-WoP that determines VM capacity and VM collocation possibilities for a given set of application workloads. We perform an empirical analysis of the approach on a set of business application workloads obtained from geographically distributed data centers. The iCirrus-WoP tool determines the fixed reserved capacity and a shared capacity of a VM which it can share with another collocated VM. Based on the workload variation, the tool determines if the VM should be statically allocated or needs a dynamic placement. To determine the collocation possibility, iCirrus-WoP performs a peak utilization analysis of the workloads. The empirical analysis reveals the possibility of collocating applications running in different time-zones. The VM capacity that the tool recommends, show a possibility of improving the overall utilization of the infrastructure by more than 70% if they are appropriately collocated.
Low Complexity Layered Division Multiplexing for ATSC 3.0

In this paper, we propose novel transmitter and receiver architectures for low complexity layered division multiplexing (LDM) systems. The proposed transmitter architecture, which is adopted as a baseline technology of the Advanced Television Systems Committee 3.0, shares time and frequency interleavers, FFT, pilot patterns, guard interval, preamble, and bootstrap among different layers, so that the implementation of LDM receivers can be realized with less than 10% complexity increase compared to conventional single layer receivers. With such low complexity increment, we show simulation and laboratory test results that the proposed LDM system has significant performance advantage (3-9 dB) over traditional TDM systems, and maintains its performance up to the velocity of 260 km/h in mobile reception.
Determinants of relapse periodicity in Plasmodium vivax malaria

Plasmodium vivax is a major cause of febrile illness in endemic areas of Asia, Central and South America, and the horn of Africa. Plasmodium vivax infections are characterized by relapses of malaria arising from persistent liver stages of the parasite (hypnozoites) which can be prevented only by 8-aminoquinoline anti-malarials. Tropical P. vivax relapses at three week intervals if rapidly eliminated anti-malarials are given for treatment, whereas in temperate regions and parts of the sub-tropics P. vivax infections are characterized either by a long incubation or a long-latency period between illness and relapse - in both cases approximating 8-10 months. The epidemiology of the different relapse phenotypes has not been defined adequately despite obvious relevance to malaria control and elimination. The number of sporozoites inoculated by the anopheline mosquito is an important determinant of both the timing and the number of relapses. The intervals between relapses display a remarkable periodicity which has not been explained. Evidence is presented that the proportion of patients who have successive relapses is relatively constant and that the factor which activates hypnozoites and leads to regular interval relapse in vivax malaria is the systemic febrile illness itself. It is proposed that in endemic areas a large proportion of the population harbours latent hypnozoites which can be activated by a systemic illness such as vivax or falciparum malaria. This explains the high rates of vivax following falciparum malaria, the high proportion of heterologous genotypes in relapses, the higher rates of relapse in people living in endemic areas compared with artificial infection studies, and, by facilitating recombination between different genotypes, contributes to P. vivax genetic diversity particularly in low transmission settings. Long-latency P. vivax phenotypes may be more widespread and more prevalent than currently thought. These observations have important implications for the assessment of radical treatment efficacy and for malaria control and elimination.
CQASUMM: Building References for Community Question Answering Summarization Corpora

Answers submitted to CQA forums are often elaborate, contain spam, are marred by slurs and business promotions. It is difficult for a reader to go through numerous such answers to gauge community opinion. As a result summarization becomes a prioritized task. However, there is a dearth of neural approaches for CQA summarization due to the lack of large scale annotated dataset. We create CQASUMM, the first annotated CQA summarization dataset by filtering the 4.4 million Yahoo! Answers L6 dataset. We sample threads where the best answer can double up as a reference and build hundred word summaries from them. We provide scripts1 to reconstruct the dataset and introduce the new task of Community Question Answering Summarization.
 Multi document summarization(MDS) has been widely studied using news corpora. However documents in CQA have higher variance and contradicting opinion. We compare the popular MDS techniques and evaluate their performance on our CQA corpora. We find that most MDS workflows are built for the entirely factual news corpora, whereas our corpus has a fair share of opinion based instances too. We therefore introduce OpinioSumm, a new MDS which outperforms the best baseline by 4.6% w.r.t ROUGE-1 score.
The accessory coracobrachialis muscle: ultrasound and MR features

To present the prevalence, clinical relevance, and ultrasound (US) and magnetic resonance imaging (MRI) appearances of the accessory coracobrachialis (ACB) muscle. We present an US prospective study of the ACB muscle over a 2-year period. Five of the eight patients with suspected ACB on US were subsequently examined by MRI. An ACB muscle was demonstrated by US in eight patients (eight shoulders), including seven females, one male, with mean age 39 years, over 770 (664 patients) consecutive shoulder US examinations referred to our institution yielding a prevalence of 1.04 %. In dynamic US assessment, one case of subcoracoid impingement secondary to a bulky ACB was diagnosed. No thoracic outlet syndrome was encountered in the remaining cases. MRI confirmed the presence of the accessory muscle in five cases. ACB muscle is a rarely reported yet not uncommon anatomic variation of the shoulder musculature encountered only in eight of 664 patients referred for shoulder US study. Its US and MRI appearance is described. One of our patients presented with subcoracoid impingement related to the presence of an ACB.
Language Recognition via i-vectors and Dimensionality Reduction

In this paper, a new language identification system is presented based on the total variability approach previously developed in the field of speaker identification. Various techniques are employed to extract the most salient features in the lower dimensional i-vector space and the system developed results in excellent performance on the 2009 LRE evaluation set without the need for any post-processing or backend techniques. Additional performance gains are observed when the system is combined with other acoustic systems.
Effects of diet on behaviour and cognition in children.

Diet can affect cognitive ability and behaviour in children and adolescents. Nutrient composition and meal pattern can exert immediate or long-term, beneficial or adverse effects. Beneficial effects mainly result from the correction of poor nutritional status. For example, thiamin treatment reverses aggressiveness in thiamin-deficient adolescents. Deleterious behavioural effects have been suggested; for example, sucrose and additives were once suspected to induce hyperactivity, but these effects have not been confirmed by rigorous investigations. In spite of potent biological mechanisms that protect brain activity from disruption, some cognitive functions appear sensitive to short-term variations of fuel (glucose) availability in certain brain areas. A glucose load, for example, acutely facilitates mental performance, particularly on demanding, long-duration tasks. The mechanism of this often described effect is not entirely clear. One aspect of diet that has elicited much research in young people is the intake/omission of breakfast. This has obvious relevance to school performance. While effects are inconsistent in well-nourished children, breakfast omission deteriorates mental performance in malnourished children. Even intelligence scores can be improved by micronutrient supplementation in children and adolescents with very poor dietary status. Overall, the literature suggests that good regular dietary habits are the best way to ensure optimal mental and behavioural performance at all times. Then, it remains controversial whether additional benefit can be gained from acute dietary manipulations. In contrast, children and adolescents with poor nutritional status are exposed to alterations of mental and/or behavioural functions that can be corrected, to a certain extent, by dietary measures.
Visual Exploration of High Dimensional Scalar Functions

An important goal of scientific data analysis is to understand the behavior of a system or process based on a sample of the system. In many instances it is possible to observe both input parameters and system outputs, and characterize the system as a high-dimensional function. Such data sets arise, for instance, in large numerical simulations, as energy landscapes in optimization problems, or in the analysis of image data relating to biological or medical parameters. This paper proposes an approach to analyze and visualizing such data sets. The proposed method combines topological and geometric techniques to provide interactive visualizations of discretely sampled high-dimensional scalar fields. The method relies on a segmentation of the parameter space using an approximate Morse-Smale complex on the cloud of point samples. For each crystal of the Morse-Smale complex, a regression of the system parameters with respect to the output yields a curve in the parameter space. The result is a simplified geometric representation of the Morse-Smale complex in the high dimensional input domain. Finally, the geometric representation is embedded in 2D, using dimension reduction, to provide a visualization platform. The geometric properties of the regression curves enable the visualization of additional information about each crystal such as local and global shape, width, length, and sampling densities. The method is illustrated on several synthetic examples of two dimensional functions. Two use cases, using data sets from the UCI machine learning repository, demonstrate the utility of the proposed approach on real data. Finally, in collaboration with domain experts the proposed method is applied to two scientific challenges. The analysis of parameters of climate simulations and their relationship to predicted global energy flux and the concentrations of chemical species in a combustion simulation and their integration with temperature.
Dopaminergic Contributions to Vocal Learning.

Although the brain relies on auditory information to calibrate vocal behavior, the neural substrates of vocal learning remain unclear. Here we demonstrate that lesions of the dopaminergic inputs to a basal ganglia nucleus in a songbird species (Bengalese finches, Lonchura striata var. domestica) greatly reduced the magnitude of vocal learning driven by disruptive auditory feedback in a negative reinforcement task. These lesions produced no measureable effects on the quality of vocal performance or the amount of song produced. Our results suggest that dopaminergic inputs to the basal ganglia selectively mediate reinforcement-driven vocal plasticity. In contrast, dopaminergic lesions produced no measurable effects on the birds' ability to restore song acoustics to baseline following the cessation of reinforcement training, suggesting that different forms of vocal plasticity may use different neural mechanisms.



During skill learning, the brain relies on sensory feedback to improve motor performance. However, the neural basis of sensorimotor learning is poorly understood. Here, we investigate the role of the neurotransmitter dopamine in regulating vocal learning in the Bengalese finch, a songbird with an extremely precise singing behavior that can nevertheless be reshaped dramatically by auditory feedback. Our findings show that reduction of dopamine inputs to a region of the songbird basal ganglia greatly impairs vocal learning but has no detectable effect on vocal performance. These results suggest a specific role for dopamine in regulating vocal plasticity.
Laparoscopic versus open repair of paraesophageal hernia: the second decade.

A decade ago we reported that laparoscopic repair of paraesophageal hernia (PEH) had an objective recurrence rate of 42% compared with 15% after open repair. Since that report we have modified our laparoscopic technique. The aim of this study was to determine if these modifications have reduced the rate of objective hernia recurrence.



We retrospectively identified all patients that had primary repair of a PEH with ≥ 50% of the stomach in the chest from May 1998 to January 2010 with objective follow-up by videoesophagram. The finding of any size of hernia was considered to be recurrence.



There were 73 laparoscopic and 73 open PEH repairs that met the study criteria. There were no significant differences in gender, body mass index, or prevalence of a comorbid condition between groups. The median follow-up was similar (12 months laparoscopic versus 16 months open; p = 0.11). In the laparoscopic group, 84% of patients had absorbable mesh reinforcement of the crural closure and 40% had a Collis gastroplasty, compared with 32% and 26%, respectively, in the open group. A recurrent hernia was identified in 27 patients (18%), 9 after laparoscopic repair and 18 after open repair (p = 0.09). The median size of a recurrent hernia was 3 cm, and the incidence of recurrence increased yearly in those with serial follow-up with no early peak or late plateau.



In our first decade of laparoscopic PEH repair, no mesh crural reinforcement was used, and no patient had a Collis gastroplasty. Evolution in the technique of laparoscopic PEH repair during the subsequent decade has reduced the hernia recurrence rate to that seen with an open approach. Reduced morbidity and shorter hospital stay make laparoscopy the preferred approach, but continued efforts to reduce hernia recurrence are warranted.
Any-Angle Pathfinding for Multiple Agents Based on SIPP Algorithm

The problem of finding conflict-free trajectories for multiple agents of identical circular shape, operating in shared 2D workspace, is addressed in the paper and decoupled, e.g., prioritized, approach is used to solve this problem. Agents’ workspace is tessellated into the square grid on which anyangle moves are allowed, e.g. each agent can move into an arbitrary direction as long as this move follows the straight line segment whose endpoints are tied to the distinct grid elements. A novel any-angle planner based on Safe Interval Path Planning (SIPP) algorithm is proposed to find trajectories for an agent moving amidst dynamic obstacles (other agents) on a grid. This algorithm is then used as part of a prioritized multi-agent planner AA-SIPP(m). On the theoretical side, we show that AA-SIPP(m) is complete under well-defined conditions. On the experimental side, in simulation tests with up to 250 agents involved, we show that our planner finds much better solutions in terms of cost (up to 20%) compared to the planners relying on cardinal moves only.
Prioritizing Bellman Backups without a Priority Queue

Several researchers have shown that the efficiency of value iteration, a dynamic programming algorithm for Markov decision processes, can be improved by prioritizing the order of Bellman backups to focus computation on states where the value function can be improved the most. In previous work, a priority queue has been used to order backups. Although this incurs overhead for maintaining the priority queue, previous work has argued that the overhead is usually much less than the benefit from prioritization. However this conclusion is usually based on a comparison to a non-prioritized approach that performs Bellman backups on states in an arbitrary order. In this paper, we show that the overhead for maintaining the priority queue can be greater than the benefit, when it is compared to very simple heuristics for prioritizing backups that do not require a priority queue. Although the order of backups induced by our simple approach is often sub-optimal, we show that its smaller overhead allows it to converge faster than other state-of-the-art priority-based solvers.