nils-herrmann/clean_scirepeval huggingface dataset:
A General Formulation for Safely Exploiting Weakly Supervised Data

Weakly supervised data is an important machine learning data to help improve learning performance. However, recent results indicate that machine learning techniques with the usage of weakly supervised data may sometimes cause performance degradation. Safely leveraging weakly supervised data is important, whereas there is only very limited effort, especially on a general formulation to help provide insight to guide safe weakly supervised learning. In this paper we present a scheme that builds the final prediction results by integrating several weakly supervised learners. Our resultant formulation brings two advantages. i) For the commonly used convex loss functions in both regression and classification tasks, safeness guarantees exist under a mild condition; ii) Prior knowledge related to the weights of base learners can be embedded in a flexible manner. Moreover, the formulation can be addressed globally by simple convex quadratic or linear program efficiently. Experiments on multiple weakly supervised learning tasks such as label noise learning, domain adaptation and semi-supervised learning validate the effectiveness.
The York-Mason technique for recto-urethral fistulas.

Recto-urethral fistula formation following radical prostatectomy is an uncommon but potentially devastating event. There is no consensus in the literature regarding the treatment of these fistulas. We present here our experiences treating recto-urethral fistulas.



We analyzed 8 cases of rectourethral fistula treated at our institution in the last seven years. Seven of the patients underwent repair of the fistula using the modified York-Mason procedure.



The causes of the fistula were radical retropubic prostatectomy in five patients, perineal debridement of Fournier's gangrene in one, transvesical prostatectomy in one and transurethral resection of the prostate in the other patient. The most common clinical manifestation was fecaluria, present in 87.5% of the cases. The mean time elapsed between diagnosis and correction of the fistula was 29.6 (7-63) months. One spontaneous closure occurred after five months of delayed catheterization. Urinary and retrograde urethrocystography indicated the site of the fistula in 71.4% of the cases. No patient presented recurrence of the fistula after its correction with the modified York-Mason procedure.



The performance of routine colostomy and cystostomy is unnecessary. The technique described by York-Mason permits easy access, reduces surgical and hospitalization times and presents low complication and morbidity rates when surgically correcting recto-urethral fistulas.
Population dynamics of Aurelia sp.1 ephyrae and medusae in Jiaozhou Bay, China

The scyphozoan Aurelia aurita (Linnaeus) s. l., is a cosmopolitan species-complex which blooms seasonally in a variety of coastal and shelf sea environments around the world. We hypothesized that ephyrae of Aurelia sp.1 are released from the inner part of the Jiaozhou Bay, China when water temperature is below 15°C in late autumn and winter. The seasonal occurrence, growth, and variation of the scyphomedusa Aurelia sp.1 were investigated in Jiaozhou Bay from January 2011 to December 2011. Ephyrae occurred from May through June with a peak abundance of 2.38 ± 0.56 ind/m3 in May, while the temperature during this period ranged from 12 to 18°C. The distribution of ephyrae was mainly restricted to the coastal area of the bay, and the abundance was higher in the dock of the bay than at the other inner bay stations. Young medusae derived from ephyrae with a median diameter of 9.74 ± 1.7 mm were present from May 22. Growth was rapid from May 22 to July 2 with a maximum daily growth rate of 39%. Median diameter of the medusae was 161.80 ± 18.39 mm at the beginning of July. In August, a high proportion of deteriorated specimens was observed and the median diameter decreased. The highest average abundance is 0.62 ± 1.06 ind/km2 in Jiaozhou Bay in August. The abundance of Aurelia sp.1 medusae was low from September and then decreased to zero. It is concluded that water temperature is the main driver regulating the life cycle of Aurelia sp.1
Systematic evaluation of spliced alignment programs for RNA-seq data

High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.
Acquisition of the algorithms of social life: a domain-based approach.

Proposing that the algorithms of social life are acquired as a domain-based process, the author offers distinctions between social domains preparing the individual for proximity-maintenance within a protective relationship (attachment domain), use and recognition of social dominance (hierarchical power domain), identification and maintenance of the lines dividing "us" and "them" (coalitional group domain), negotiation of matched benefits with functional equals (reciprocity domain), and selection and protection of access to sexual partners (mating domain). Flexibility in the implementation of domains occurs at 3 different levels: versatility at a bioecological level, variations in the cognitive representation of individual experience, and cultural and individual variations in the explicit management of social life. Empirical evidence for domain specificity was strongest for the attachment domain; supportive evidence was also found for the distinctiveness of the 4 other domains. Implications are considered at theoretical and applied levels.
Simulation model of DVB-S2 system

This paper presents simulation model of the DVB-S2 (Digital Video Broadcasting - Satellite - Second Generation) system implemented in Simulink, Matlab. The model provides simulation of the DVB-S2 system parameters in AWGN (Additive White Gaussian Noise) channel. The aim of this model is to propose optimal DVB-S2 parameters in different propagation conditions. The simulation offers two modulation scheme options QPSK (Quadrature Phase Shift Keying) and 8PSK (8 Phase Shift Keying) with different code ratio values. During the simulation, BER (bit error rate) and PER (packet error rate) are calculated and the constellation diagram is observed. Simulation results, obtained by using two test images with different texture, showed that QPSK modulation is more robust compared to 8PSK modulation in the same propagation conditions. Simulink model results were compared with measurements of several Astra 1 satellite (19,2° E) transponders parameters. Lab-measured values achieved higher SNR values than simulation cases because of real wireless channel conditions. Optimal operation parameters for a DVB-S2 system according to channel conditions and the required bit rate are proposed.
Complex shoulder disorders: evaluation and treatment.

Evaluation of patients with shoulder disorders often presents challenges. Among the most troublesome are revision surgery in patients with massive rotator cuff tear, atraumatic shoulder instability, revision arthroscopic stabilization surgery, adhesive capsulitis, and bicipital and subscapularis injuries. Determining functional status is critical before considering surgical options in the patient with massive rotator cuff tear. When nonsurgical treatment of atraumatic shoulder stability is not effective, inferior capsular shift is the treatment of choice. Arthroscopic revision of failed arthroscopic shoulder stabilization procedures may be undertaken when bone and tissue quality are good. Arthroscopic release is indicated when idiopathic adhesive capsulitis does not respond to nonsurgical treatment; however, results of both nonsurgical and surgical treatment of posttraumatic and postoperative adhesive capsulitis are often disappointing. Patients not motivated to perform the necessary postoperative therapy following subscapularis repair are best treated with arthroscopic débridement and biceps tenotomy.
Viral Marketing for Multiple Products

Viral Marketing, the idea of exploiting social interactions of users to propagate awareness for products, has gained considerable focus in recent years. One of the key issues in this area is to select the best seeds that maximize the influence propagated in the social network. In this paper, we define the seed selection problem (called t-Influence Maximization, or t-IM) for multiple products. Specifically, given the social network and t products along with their seed requirements, we want to select seeds for each product that maximize the overall influence. As the seeds are typically sent promotional messages, to avoid spamming users, we put a hard constraint on the number of products for which any single user can be selected as a seed. In this paper, we design two efficient techniques for the t-IM problem, called Greedy and FairGreedy. The Greedy algorithm uses simple greedy hill climbing, but still results in a 1/3-approximation to the optimum. Our second technique, FairGreedy, allocates seeds with not only high overall influence (close to Greedy in practice), but also ensures fairness across the influence of different products. We also design efficient heuristics for estimating the influence of the selected seeds, that are crucial for running the seed selection on large social network graphs. Finally, using extensive simulations on real-life social graphs, we show the effectiveness and scalability of our techniques compared to existing and naive strategies.
VineSens: An Eco-Smart Decision-Support Viticulture System

This article presents VineSens, a hardware and software platform for supporting the decision-making of the vine grower. VineSens is based on a wireless sensor network system composed by autonomous and self-powered nodes that are deployed throughout a vineyard. Such nodes include sensors that allow us to obtain detailed knowledge on different viticulture processes. Thanks to the use of epidemiological models, VineSens is able to propose a custom control plan to prevent diseases like one of the most feared by vine growers: downy mildew. VineSens generates alerts that warn farmers about the measures that have to be taken and stores the historical weather data collected from different spots of the vineyard. Such data can then be accessed through a user-friendly web-based interface that can be accessed through the Internet by using desktop or mobile devices. VineSens was deployed at the beginning in 2016 in a vineyard in the Ribeira Sacra area (Galicia, Spain) and, since then, its hardware and software have been tested to prevent the development of downy mildew, showing during its first season that the system can led to substantial savings, to decrease the amount of phytosanitary products applied, and, as a consequence, to obtain a more ecologically sustainable and healthy wine.
Blur-Invariant Deep Learning for Blind-Deblurring

In this paper, we investigate deep neural networks for blind motion deblurring. Instead of regressing for the motion blur kernel and performing non-blind deblurring outside of the network (as most methods do), we propose a compact and elegant end-to-end deblurring network. Inspired by the data-driven sparse-coding approaches that are capable of capturing linear dependencies in data, we generalize this notion by embedding non-linearities into the learning process. We propose a new architecture for blind motion deblurring that consists of an autoencoder that learns the data prior, and an adversarial network that attempts to generate and discriminate between clean and blurred features. Once the network is trained, the generator learns a blur-invariant data representation which when fed through the decoder results in the final deblurred output.
ARM Virtualization: Performance and Architectural Implications

ARM servers are becoming increasingly common, making server technologies such as virtualization for ARM of growing importance. We present the first study of ARM virtualization performance on server hardware, including multicore measurements of two popular ARM and x86 hypervisors, KVM and Xen. We show how ARM hardware support for virtualization can enable much faster transitions between VMs and the hypervisor, a key hypervisor operation. However, current hypervisor designs, including both Type 1 hypervisors such as Xen and Type 2 hypervisors such as KVM, are not able to leverage this performance benefit for real application workloads. We discuss the reasons why and show that other factors related to hypervisor software design and implementation have a larger role in overall performance. Based on our measurements, we discuss changes to ARM's hardware virtualization support that can potentially bridge the gap to bring its faster VM-to-hypervisor transition mechanism to modern Type 2 hypervisors running real applications. These changes have been incorporated into the latest ARM architecture.
Secure and Lightweight Authentication Protocol for NFC Tag Based Services

Near Field Communication(NFC) technology is one of the most promising technologies in the field of mobile application services recently. The integration of NFC technology and smart mobile device (e.g., smart phones, tablet PC and etc.) stimulates the daily increasing popularity of NFC-based mobile applications which having proliferated in the mobile society. However, this proliferation of NFC-based mobile services in a mobile environment can cause another security threat in the field of mobile application services. Recently, mobile phishing and smishing are one of the most serious security issues in the mobile application services. And, the NFC tag-based mobile services (i.e. NFC tag based services) also have the same problem because an NFC tag have security vulnerabilities. Actually, NFC-enabled device can communicate with NFC tag using specified data format, be called NFC Data Exchange Format(NDEF). The NDEF message is composed one or more NDEF records such as text, URI, Smart post(text and URL) and so on. Therefore, if an attacker overwrite the NDEF message in a tag or replace a NFC tag with hacked tag, they might deliver a mobile malware to an NFC-enabled device. In this paper, a secure and lightweight authentication protocols for NFC tag based services is proposed which effectively achieves security with preventing spoofing, DoS, data modification and phishing attack. And, this authentication protocols are also requires less memory storage and computational power for low-cost NFC tags.
Weakly Supervised Slot Tagging with Partially Labeled Sequences from Web Search Click Logs

In this paper, we apply a weakly-supervised learning approach for slot tagging using conditional random fields by exploiting web search click logs. We extend the constrained lattice training of Täckström et al. (2013) to non-linear conditional random fields in which latent variables mediate between observations and labels. When combined with a novel initialization scheme that leverages unlabeled data, we show that our method gives significant improvement over strong supervised and weakly-supervised baselines.
Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules

The absence of a comprehensive database of locations where bacteria live is an important obstacle for biologists to understand and study the interactions between bacteria and their habitats. This paper reports the results to a challenge, set forth by the Bacteria Biotopes Task of the BioNLP Shared Task 2013. Two systems are explained: Sub-task 1 system for identifying habitat mentions in unstructured biomedical text and normalizing them through the OntoBiotope ontology and Sub-task 2 system for extracting localization and partof relations between bacteria and habitats. Both approaches rely on syntactic rules designed by considering the shallow linguistic analysis of the text. Sub-task 2 system also makes use of discourse-based rules. The two systems achieve promising results on the shared task test data set.
MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling.

The epidermal growth factor receptor (EGFR) kinase inhibitors gefitinib and erlotinib are effective treatments for lung cancers with EGFR activating mutations, but these tumors invariably develop drug resistance. Here, we describe a gefitinib-sensitive lung cancer cell line that developed resistance to gefitinib as a result of focal amplification of the MET proto-oncogene. inhibition of MET signaling in these cells restored their sensitivity to gefitinib. MET amplification was detected in 4 of 18 (22%) lung cancer specimens that had developed resistance to gefitinib or erlotinib. We find that amplification of MET causes gefitinib resistance by driving ERBB3 (HER3)-dependent activation of PI3K, a pathway thought to be specific to EGFR/ERBB family receptors. Thus, we propose that MET amplification may promote drug resistance in other ERBB-driven cancers as well.
A sliding mode missile pitch autopilot synthesis for high angle of attack maneuvering

A new approach to the synthesis of longitudinal autopilots for missiles flying at high angle of attack regimes is presented. The methodology is based on sliding mode control, and uses a combination of aerodynamic surfaces and reaction jet thrusters, to achieve controllability beyond stall. The autopilot is tested on a small section of the flight envelope consisting of a fast 180 heading reversal in the vertical plane, which requires robustness with respect to uncertainties in the system’s dynamics induced by large variations in dynamic pressure and aerodynamic coefficients. Nonlinear simulation results show excellent performance and capabilities of the control system structure.
Aeromonas hydrophila produces conductive nanowires.

Aeromonas hydrophila is a facultative anaerobe which, under conditions of oxygen depletion, uses Fe(III) as electron acceptor. A. hydrophila produces pili during growth with Fe(III). The study was focused on the characterization of the morphology, the electrical properties and the nature of the bacterial pili. Scanning electron microscopy and conductive-probe atomic force microscopy revealed the presence of filaments between cells and substrate and their conductive nature. Our results indicate that pili of A. hydrophila strain A might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(III) oxides and, in addition, the possibility of playing a role in inter/intra species signaling. Quorum sensing (QS) is recognized as one of the main regulatory ways for extracellular polymeric substances (EPS) production and biofilm formation. We present evidence that nanowire formation can be regulated by addition of synthetic acyl-homoserine lactones (AHL). These conductive pili may be involved in various interactions, and their protein components might be usable in the future for biotechnological approaches in materials science.
Iatrogenic retinal artery occlusion caused by cosmetic facial filler injections.

To investigate the clinical manifestations and visual prognosis of retinal artery occlusion resulting from cosmetic facial filler injections.



Retrospective, noncomparative case series.



Setting. Institutional. Study Population. Twelve consecutive patients with retinal artery occlusion caused by cosmetic facial filler injections.  Filler materials, injection sites, best-corrected visual acuities, fundus fluorescein angiography and optical coherence tomography findings, and associated ocular and systemic manifestations.



Seven, 2, and 3 patients had ophthalmic, central retinal, and branch retinal artery occlusions, respectively. Injected materials included autologous fat (7 cases), hyaluronic acid (4 cases), and collagen (1 case), and injection sites were the glabellar region (7 cases), nasolabial fold (4 cases), or both (1 case). Injected autologous fat was associated with worse final best-corrected visual acuity than the other materials. All patients with ophthalmic artery occlusion had ocular pain and no improvement in best-corrected visual acuity. Optical coherence tomography revealed thinner and less vascular choroids in eyes with ophthalmic artery occlusion than in adjacent normal eyes. Concomitant brain infarction developed in 2 cases each of central retinal artery occlusion and ophthalmic artery occlusion. Phthisis developed in 1 case of ophthalmic artery occlusion.



Cosmetic filler injections into the glabellar region or nasolabial fold can cause retinal artery occlusion. Iatrogenic ophthalmic artery occlusion is associated with painful blindness, a thin choroid, brain infarction, and poor visual outcomes, particularly when autologous fat is used. Ophthalmic examination and systematic brain magnetic resonance imaging should be performed in patients with ocular pain after such injections.
Tomato Lycopene : Functional Proprieties and Health Benefits

The growing concerns for physical wellbeing and health have been reflected in the way we choose food in our table. Nowadays, we are all more informed consumers and choose healthier foods. On the other hand, stroke, cancer and atherosclerosis may be somehow minimized by the intake of some bioactive compounds present in food, the so-called nutraceuticals and functional foods. The aim of this work was to make a revision of the published studies about the effects of some bioactive compounds, namely lycopene in human health, in the prevention of diseases, thus playing the role of a functional food. Free radical in human body can induce cell damage and consequently can be responsible for the development of some cancers and chronic diseases. Lycopene is one of the most powerful antioxidants known, being the predominant carotenoid in tomato. The respective chemistry, bioavailability, and its functional role in the prevention of several diseases will be object of this work. On the other hand, the inclusion of lycopene in some foods can also be made by biotechnology and represents a way to recover the wastes in the tomato industry with nutritional positive effects in health. Tomato, lycopene, bioavailability, functional foods, carotenoids, cancer and antioxidants.