nils-herrmann/clean_scirepeval huggingface dataset:
Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1) as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2). We also identified two genes (DNAH5, OFD1) with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5). Our analytical strategy highlights the utility of bioinformatic resources, including human disease records and model organism phenotyping, in novel gene discovery for rare human disease. The results underscore the extensive genetic heterogeneity underlying non-syndromic LSLs, and posit potential novel candidate genes and complex modes of inheritance in this important group of birth defects.
KittingBot: A Mobile Manipulation Robot for Collaborative Kitting in Automotive Logistics

Individualized manufacturing of cars requires kitting: the collection of individual sets of part variants for each car. This challenging logistic task is frequently performed manually by warehouseman. We propose a mobile manipulation robotic system for autonomous kitting, building on the Kuka Miiwa platform which consists of an omnidirectional base, a 7 DoF collaborative iiwa manipulator, cameras, and distance sensors. Software modules for detection and pose estimation of transport boxes, part segmentation in these containers, recognition of part variants, grasp generation, and arm trajectory optimization have been developed and integrated. Our system is designed for collaborative kitting, i.e. some parts are collected by warehouseman while other parts are picked by the robot. To address safe human-robot collaboration, fast arm trajectory replanning considering previously unforeseen obstacles is realized. The developed system was evaluated in the European Robotics Challenge 2, where the Miiwa robot demonstrated autonomous kitting, part variant recognition, and avoidance of unforeseen obstacles.
Peniscopically controlled CO2 laser excision for conservative treatment of in situ and T1 penile carcinoma: report on 224 patients.

To evaluate the outcome of peniscopically controlled laser excision of early-stage penile carcinoma.



Patients treated from 1982 to 2006 were investigated. The primary treatment was excisional surgery alone for in situ or initially invasive flat tumors, and reductive chemotherapy followed by surgery for the exophytic lesions. All excisional procedures were conducted by CO(2) laser under peniscopic control.



Of a total of 224 patients, 111 underwent partial excision of the glans and/or coronal sulcus surface, and 113 total surface excision. Forty patients underwent reductive chemotherapy. Complete excision was obtained in 221 cases (98.7%) at lateral margins and in 217 cases (96.9%) at deep margin. Postoperative complications were negligible. Overall, the 10-yr recurrence rate was 17.5% (95% confidence interval, 16.4-18.6%), and apparently was not affected by the in situ or invasive nature of the lesion. Amputation was required in nine patients, for a 10-yr amputation rate of 5.5% (range, 5.2-5.7%). In the remaining cases, organ form and curvature were preserved, with satisfactory cosmetic and functional results.



Early-stage penile carcinomas can be effectively treated with the organ-sparing strategy described here. Because local recurrences occur in a minority of patients and can be safely treated, organ preservation is compatible with local disease control. Reductive systemic chemotherapy in selected exophytic cases broadens the indication for our conservative approach.
Ankle syndesmosis: a qualitative and quantitative anatomic analysis.

Syndesmosis sprains can contribute to chronic pain and instability, which are often indications for surgical intervention. The literature lacks sufficient objective data detailing the complex anatomy and localized osseous landmarks essential for current surgical techniques.



To qualitatively and quantitatively analyze the anatomy of the 3 syndesmotic ligaments with respect to surgically identifiable bony landmarks.



Descriptive laboratory study.



Sixteen ankle specimens were dissected to identify the anterior inferior tibiofibular ligament (AITFL), posterior inferior tibiofibular ligament (PITFL), interosseous tibiofibular ligament (ITFL), and bony anatomy. Ligament lengths, footprints, and orientations were measured in reference to bony landmarks by use of an anatomically based coordinate system and a 3-dimensional coordinate measuring device.



The syndesmotic ligaments were identified in all specimens. The pyramidal-shaped ITFL was the broadest, originating from the distal interosseous membrane expansion, extending distally, and terminating 9.3 mm (95% CI, 8.3-10.2 mm) proximal to the central plafond. The tibial cartilage extended 3.6 mm (95% CI, 2.8-4.4 mm) above the plafond, a subset of which articulated directly with the fibular cartilage located 5.2 mm (95% CI, 4.6-5.8 mm) posterior to the anterolateral corner of the tibial plafond. The primary AITFL band(s) originated from the tibia 9.3 mm (95% CI, 8.6-10.0 mm) superior and medial to the anterolateral corner of the tibial plafond and inserted on the fibula 30.5 mm (95% CI, 28.5-32.4 mm) proximal and anterior to the inferior tip of the lateral malleolus. Superficial fibers of the PITFL originated along the distolateral border of the posterolateral tubercle of the tibia 8.0 mm (95% CI, 7.5-8.4 mm) proximal and medial to the posterolateral corner of the plafond and inserted along the medial border of the peroneal groove 26.3 mm (95% CI, 24.5-28.1 mm) superior and posterior to the inferior tip of the lateral malleolus.



The qualitative and quantitative anatomy of the syndesmotic ligaments was reproducibly described and defined with respect to surgically identifiable bony prominences.



Data regarding anatomic attachment sites and distances to bony prominences can optimize current surgical fixation techniques, improve anatomic restoration, and reduce the risk of iatrogenic injury from malreduction or misplaced implants. Quantitative data also provide the consistency required for the development of anatomic reconstructions.
Heuristics for the Assortment Planning Problem under Ranking-based Consumer Choice Models

We model a retailer’s assortment planning problem under a ranking-based choice model of consumer preferences. Under this consumer choice model each customer belongs to a type, where a type is a ranking of the potential products by the order of preference, and the customer purchases his highest ranked product (if any) offered in the assortment. In our model we consider products with different price/cost parameters, we assume that the retailer incurs a fixed carrying cost per product offered, a substitution penalty for each customer who does not purchase his first choice and a lost sale penalty cost for each customer who leaves the store empty-handed. In the absence of any restrictions on the consumer types, searching for the optimal assortment using enumeration or integer programming is not practically feasible. The optimal assortment has very little structure so that simple greedy-type heuristics often fail to find the optimal assortment and have very poor worst case bounds. We develop an effective algorithm, called the In-Out Algorithm, which always provides an optimal solution and show numerically that it is very fast, e.g., more than 10,000 times faster than enumeration on a problem with 20 products.
Numerical Study on the Performance Effect of Solidity on the Straight-Bladed Vertical Axis Wind Turbine

The solidity is one of the most important factors which greatly affects the performance of the straight-bladed vertical axis wind turbine (SB-VAWT). In this study, numerical computations were carried out on a small model of the SB-VAWT with different solidities to invest its performance effects. Two kinds of solidity were decided, and for each one, three patterns were selected by changing the blade chord and number. Numerical computations based on the 2 dimensions incompressible steady flow were made. Flow fields around the SB-VAWT were obtained, and the torque and power coefficients were also calculated. According to the computation results under the conditions of this study, the effects of solidity on both the static and dynamic performance of the SB-VAWT were discussed. Keywords-vertical axis wind turbine;straight-bladed; numerical computation; solidity; stactic
A security evaluation of popular Internet of Things protocols for manufacturers

The Internet of Things (IoT) continues to increase in popularity as more “smart” devices are released and sold every year. Three protocols in particular, Zigbee, Z-wave, and Bluetooth Low Energy (BLE) are used for network communication on a significant number of IoT devices. However, devices utilizing each of these three protocols have been compromised due to either implementation failures by the manufacturer or security shortcomings in the protocol itself. This paper identifies the security features and shortcomings of each protocol citing employed attacks for reference. Additionally, it will serve to help manufacturers make two decisions: First, should they invest in creating their own protocol, and second, if they decide against this, which protocol should they use and how should they implement it to ensure their product is as secure as it can be. These answers are made with respect to the specific factors manufacturers in the IoT space face such as the reversed CIA model with availability usually being the most important of the three and the ease of use versus security tradeoff that manufacturers have to consider. This paper finishes with a section aimed at future research for IoT communication protocols.
Interactive cage generation for mesh deformation

Many previous efforts have been focused on generating optimal coordinates for cage deformation; cage generation for 3D models has been relatively understudied. We introduce an efficient complete pipeline to generate high quality cages for 3D models with arbitrary topological complexities, including high genus models and those without perceptible skeletal structures. Specifically, starting from user-specified cut slides, our method automatically optimizes the consistent, orthogonal orientations of cage cross sections. Then, through automated cage meshing and refining, it can further improve the cage quality by tackling the cage coverage issue and bounding the input model with a controllable tightness. Our experiments demonstrate this approach is efficient and robust to handle a variety of 3D models including human-like, animal, and high genus models.
DICOM relay over the cloud

Healthcare institutions worldwide have adopted picture archiving and communication system (PACS) for enterprise access to images, relying on Digital Imaging Communication in Medicine (DICOM) standards for data exchange. However, communication over a wider domain of independent medical institutions is not well standardized. A DICOM-compliant bridge was developed for extending and sharing DICOM services across healthcare institutions without requiring complex network setups or dedicated communication channels. A set of DICOM routers interconnected through a public cloud infrastructure was implemented to support medical image exchange among institutions. Despite the advantages of cloud computing, new challenges were encountered regarding data privacy, particularly when medical data are transmitted over different domains. To address this issue, a solution was introduced by creating a ciphered data channel between the entities sharing DICOM services. Two main DICOM services were implemented in the bridge: Storage and Query/Retrieve. The performance measures demonstrated it is quite simple to exchange information and processes between several institutions. The solution can be integrated with any currently installed PACS-DICOM infrastructure. This method works transparently with well-known cloud service providers. Cloud computing was introduced to augment enterprise PACS by providing standard medical imaging services across different institutions, offering communication privacy and enabling creation of wider PACS scenarios with suitable technical solutions.
IR night vision video-based estimation of heart and respiration rates

With the aging of the population, comes increased incidence of chronic diseases affecting the cardiac and respiratory systems. Monitoring of these chronic conditions at home via family members or in institutions via healthcare providers is usually adequate during the day. Non-intrusive video-based monitoring approaches have been proposed using optical cameras whose performance significantly deteriorates in low light conditions. This paper proposed the use of infrared night vision cameras to monitor the heart and respiration rates in low light conditions and in complete darkness. An infrared camera in conjunction with video magnification method is used to capture and analyze the video of subjects in dark conditions. To validate the extracted heart rate, a finger photoplethysmograph (PPG) device that can display the real-time heart rate was used. To validate the respiration rate a BioHarness chest strap was used. The proposed framework was tested on different sizes of regions of interest (ROIs) and different distances between the subject and the camera. A post-processing procedure was applied on the video magnification signal to reduce noise. To characterize and rule out artifacts, an experiment on inanimate objects was also conducted. Results indicate that the non-intrusive approach based on infrared night vision cameras and video magnification method can accurately extract heart and respiration rates, and can be used for continuous healthcare monitoring in the night.
Cost-Effective Active Learning from Diverse Labelers

In traditional active learning, there is only one labeler that always returns the ground truth of queried labels. However, in many applications, multiple labelers are available to offer diverse qualities of labeling with different costs. In this paper, we perform active selection on both instances and labelers, aiming to improve the classification model most with the lowest cost. While the cost of a labeler is proportional to its overall labeling quality, we also observe that different labelers usually have diverse expertise, and thus it is likely that labelers with a low overall quality can provide accurate labels on some specific instances. Based on this fact, we propose a novel active selection criterion to evaluate the cost-effectiveness of instance-labeler pairs, which ensures that the selected instance is helpful for improving the classification model, and meanwhile the selected labeler can provide an accurate label for the instance with a relative low cost. Experiments on both UCI and real crowdsourcing data sets demonstrate the superiority of our proposed approach on selecting cost-effective queries.
System-level performance of downlink NOMA for future LTE enhancements

This paper investigates the system-level performance of downlink non-orthogonal multiple access (NOMA) with power-domain user multiplexing at the transmitter side and successive interference canceller (SIC) on the receiver side. The goal is to clarify the performance gains of NOMA for future LTE (Long-Term Evolution) enhancements, taking into account design aspects related to the LTE radio interface such as, frequency-domain scheduling with adaptive modulation and coding (AMC), and NOMA specific functionalities such as error propagation of SIC receiver, multi-user pairing and transmit power allocation. In particular, a pre-defined user grouping and fixed per-group power allocation are proposed to reduce the overhead associated with power allocation signalling. Based on computer simulations, we show that for both wideband and subband scheduling and both low and high mobility scenarios, NOMA can still provide a hefty portion of its expected gains even with error propagation, and also when the proposed simplified user grouping and power allocation are used.
The marvels of elite sports: how to get there?

683 Br J Sports Med July 2011 Vol 45 No 9 ones who performed best in youth competitions.2 3 The reason for this is that many factors play a role; factors related to both the athlete (ie, rate of learning, training and maturation of anthropometric, physiological, technical, tactical and psychological skills) and the environment (ie, opportunities created by parents, trainers, coaches, talent development programme and the competition structure) along with a component of chance.4 For example, we know that body size is related to sports performance and that youth athletes with more advanced levels of maturity (sexual, skeletal, age at peak height velocity) are, on average, taller than peers who are more delayed in maturity status.5 Therefore, in youth sport competitions, the more mature athletes seem to perform better.6 This, however, is only a temporary advantage because when adolescence nears termination, height differences among athletes of contrasting maturity status are negligible.7 An often cited ‘rule of the thumb’ is that in order to reach expertise, at least 10 000 h of deliberate practice in a period of 10 years is needed.8 This means that talent identifi cation and development in most sports may take place during athletes’ adolescent growth spurt. Studies on the relative age effect9 support the notion that in reality many youth athletes are still identifi ed as being talented on the basis of their current rather than their future level of performance and, consequently, the best youth performers are the ones who are invited to join talent development programmes or selection teams. This implies that in our talent identifi cation system, we systematically and mistakenly fail to notice the talented athletes who may not be the best performers yet, but who have the potential to be so in the future. Moreover, we fail to provide this neglected group of athletes with extra training facilities, highly certifi ed trainers and medical supervision. Therefore, to further unravel the mystery of talent, the best way may be to longitudinally follow youth athletes throughout their sports career, from start to adulthood, measuring underlying The marvels of elite sports: how to get there? Marije T Elferink-Gemser,1,2 Geir Jordet,3 Manuel J Coelho-E-Silva,4 Chris Visscher1
Design and implementation of a visible light communications system for vehicle applications

This paper presents a visible light communication system, focusing mostly on the aspects related with the hardware design and implementation. The designed system is aimed to ensure a highly-reliable communication between a commercial LED-based traffic light and a receiver mounted on a vehicle. Enabling wireless data transfer between the road infrastructure and vehicles has the potential to significantly increase the safety and efficiency of the transportation system. The paper presents the advantages of the proposed system and explains same of the choices made in the implementation process.
Empirical studies of end-user information searching

An empirical investigation of information retrieval (IR) using the MEDLINE 1 database was carried out to study user behaviour, performance and to investigate the reasons for sub-optimal searches. The experimental subjects were drawn from two groups of final year medical students who differed in their knowledge of the search system, i.e. novice and expert users. The subjects carried out four search tasks and their recall and precision performance was recorded. Data was captured on the search strategies used, duration and logs of submitted queries. Differences were found between the groups for the performance measure of recall in only one of the four experimental tasks. Overall performance was poor. Analysis of strategies, timing data and query logs showed that there were many different causes for search failure or success. Poor searchers either gave up too quickly, employed few search terms, used only simple queries or used the wrong search terms. Good searchers persisted longer, used a larger, richer set of terms, constructed more complex queries and were more diligent in evaluating the retrieved results. However, individual performances were not correlated with all of these factors. Poor performers frequently exhibited several factors of good searcher behaviour and failed for just one reason. Overall end-user searching behaviour is complex and it appears that just one factor can cause poor performance, whereas good performance can result from sub-optimal strategies that compensate for some difficulties. The implications of the results for the design of IR interfaces are discussed.
9 steps to effective population health management.

A focus on population health management is a necessary ingredient for success under value-based payment models. As part of that effort, nine ways to embrace technology can help healthcare organizations improve population health, enhance the patient experience, and reduce costs: Use predictive analytics for risk stratification. Combine predictive modeling with algorithms for financial risk management. Use population registries to identify care gaps. Use automated messaging for patient outreach. Engage patients with automated alerts and educational campaigns. Automate care management tasks. Build programs and organize clinicians into care teams. Apply new technologies effectively. Use analytics to measure performance of organizations and providers.
A Preliminary Study on Architecting Cyber-Physical Systems

Cyber-physical systems (CPSs) are deemed as the key enablers of next generation applications. Needless to say, the design, verification and validation of cyber-physical systems reaches unprecedented levels of complexity, specially due to their sensibility to safety issues. Under this perspective, leveraging architectural descriptions to reason on a CPS seems to be the obvious way to manage its inherent complexity.
 A body of knowledge on architecting CPSs has been proposed in the past years. Still, the trends of research on architecting CPS is unclear. In order to shade some light on the state-of-the art in architecting CPS, this paper presents a preliminary study on the challenges, goals, and solutions reported so far in architecting CPSs.