LLukas22/scidocs huggingface dataset:
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

MOTIVATION
Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads.


RESULTS
We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools.


AVAILABILITY AND IMPLEMENTATION
https://github.com/lh3/minimap and https://github.com/lh3/miniasm


CONTACT
hengli@broadinstitute.org


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
4D Cubism: Modeling, Animation, and Fabrication of Artistic Shapes

This article deals with creating artistic shapes in a cubist style. The authors propose adding cubist features to (or cubification of) time-variant sculptural shapes. A new concept of a 4D cubist camera is introduced for multiple projections from 4D space-time to 3D space, and 3D printing for stop-motion animation is applied.
Global Optimization Using Interval Analysis : The One-Dimensional Case

We show how interval analysis can be used to compute the minimum value of a twice continuously differentiable function of one variable over a closed interval. When both the first and second derivatives of the function have a finite number of isolated zeros, our method never fails to find the global minimum.
The influence of soft tissue thickness on crestal bone changes around implants: a 1-year prospective controlled clinical trial.

PURPOSE
The aim of this clinical trial was to evaluate the influence of gingival tissue thickness on crestal bone loss around dental implants after a 1-year follow-up.


MATERIALS AND METHODS
Forty-six implants (23 test and 23 control) were placed in 19 patients. The test implants were placed about 2 mm supracrestally, whereas the control implants were positioned at the bone level. Before implant placement, the tissue thickness at implant sites was measured with a periodontal probe. After healing, metal-ceramic cement-retained prostheses were constructed. According to tissue thickness, the test implants were divided into A (thin) and B (thick) groups. Intraoral radiographs were performed and crestal bone changes were measured at implant placement and after 1 year.


RESULTS
Mean bone loss around the test implants in group A (thin mucosa) was 1.61 +/- 0.24 mm (SE; range, 0.9 to 3.3 mm) on the mesial and 1.28 +/- 0.167 mm (range, 0.8 to 2.1 mm) on the distal. Mean bone loss in test group B (thick mucosa) implants was 0.26 +/- 0.08 mm (range, 0.2 to 0.9 mm) on the mesial aspect and 0.09 +/- 0.05 mm (range, 0.2 to 0.6 mm) on the distal aspect. Mean bone loss around control implants was 1.8 +/- 0.164 mm (range, 0.6 to 4.0 mm) and 1.87 +/- 0.166 mm (range, 0.0 to 4.1 mm) on the mesial and distal aspects, respectively. Analysis of variance revealed a significant difference in terms of bone loss between test A (thin) and B (thick) groups on both the mesial and the distal.


CONCLUSION
Initial gingival tissue thickness at the crest may be considered as a significant influence on marginal bone stability around implants. If the tissue thickness is 2.0 mm or less, crestal bone loss up to 1.45 mm may occur, despite a supracrestal position of the implant-abutment interface.
WebPatrol: automated collection and replay of web-based malware scenarios

Traditional remote-server-exploiting malware is quickly evolving and adapting to the new web-centric computing paradigm. By leveraging the large population of (insecure) web sites and exploiting the vulnerabilities at client-side modern (complex) browsers (and their extensions), web-based malware becomes one of the most severe and common infection vectors nowadays. While traditional malware collection and analysis are mainly focusing on binaries, it is important to develop new techniques and tools for collecting and analyzing web-based malware, which should include a complete web-based malicious logic to reflect the dynamic, distributed, multi-step, and multi-path web infection trails, instead of just the binaries executed at end hosts. This paper is a first attempt in this direction to automatically collect web-based malware scenarios (including complete web infection trails) to enable fine-grained analysis. Based on the collections, we provide the capability for offline "live" replay, i.e., an end user (e.g., an analyst) can faithfully experience the original infection trail based on her current client environment, even when the original malicious web pages are not available or already cleaned. Our evaluation shows that WebPatrol can collect/cover much more complete infection trails than state-of-the-art honeypot systems such as PHoneyC [11] and Capture-HPC [1]. We also provide several case studies on the analysis of web-based malware scenarios we have collected from a large national education and research network, which contains around 35,000 web sites.
Totally Free Expansions of Matroids

The aim of this paper is to give insight into the behaviour of inequivalent representations of 3-connected matroids. An element x of a matroid M is fixed if there is no extension MŒ of M by an element xŒ such that {x, xŒ} is independent and MŒ is unaltered by swapping the labels on x and xŒ. When x is fixed, a representation of M0x extends in at most one way to a representation of M. A 3-connected matroid N is totally free if neither N nor its dual has a fixed element whose deletion is a series extension of a 3-connected matroid. The significance of such matroids derives from the theorem, established here, that the number of inequivalent representations of a 3-connected matroid M over a finite field F is bounded above by the maximum, over all totally free minors N of M, of the number of inequivalent F-representations of N. It is proved that, within a class of matroids that is closed under minors and duality, the totally free matroids can be found by an inductive search. Such a search is employed to show that, for all r \ 4, there are unique and easily described rank-r quaternary and quinternary matroids, the first being the free spike. Finally, Seymour’s Splitter Theorem is extended by showing that the sequence of 3-connected matroids from a matroid M to a minor N, whose existence is guaranteed by the theorem, may be chosen so that all deletions and contractions of fixed and cofixed elements occur in the initial segment of the sequence. © 2001
The Effect of Story-based, L1 Translation, and Whatsapp Emoticon Puzzle-Solving Techniques on Iranian Intermediate EFL Learners’ Proverb Learning

This study investigated the effect of story-based technique, L1 translation, and Whatsapp emoticon puzzle solving on EFL learners’ learning proverbs. From among 90 female intermediate level learners at two language institutes in Qom, Iran, 60 homogeneous students were chosen following the administration of a sample of Nelson proficiency test and a pre-test. The 60 participants were then assigned to three experimental groups, equal in number. The experimental group 1 was instructed using story-based technique; the experimental group 2 was taught through L1 translation; and the experimental group 3 was exposed to Whatsapp emoticon puzzle solving. Subsequently, all three groups took part in a proverb post-test similar to the pre-test. The data were analyzed by ANOVA. The results showed that Whatsapp emoticon puzzle solving was significantly the most effective, and that the students’ level of learning proverbs was influenced by story-based technique more than L1 translation technique. The findings of this study can contribute to technologyenhanced language teaching.
Research Practice into/influencing Mathematics Teaching and Learning Development: Towards a Theoretical framework based on co-learning partnerships

This paper addresses issues linking research into the classroom teaching and learning of mathematics with the growth of knowledge in mathematics teaching, developments in the practice of teaching and the enhanced learning of mathematics by students in classrooms. A basic premise is that research promotes development. The paper considers both insider and outsider research and co-learning between teachers and educators in promoting classroom inquiry. Through a consideration of elements of theory such as knowledge and inquiry in teaching and of learning as knowledge growth through research/inquiry leading to enhancement of students’ learning of mathematics, a framework is suggested. Its purposes include analysis of a research project’s contribution to teaching development and conceptualization of research which has teaching development as one of its aims. Use of the framework is exemplified through its application to reports of three mathematics education research projects in the public domain. A brief afterword links the framework to concepts in activity theory.
Cervical spinal canal stenosis: the differences between stenosis at the lower cervical and multiple segment levels

The lower cervical segments are commonly the level responsible for cervical spondylotic myelopathy; however, we rarely encounter stenosis at the upper cervical segment in a clinical setting. We assumed that there might be some differences between the pathogenetic mechanisms underlying the development of cervical canal stenosis at different segments. We performed positional MRI in the weight-bearing position for 295 consecutive symptomatic patients. All subjects were classified into four groups (A: normal; B: C3-4 stenosis; C: C5-6 stenosis; D: two-level cervical segments stenosis, stenosis at C3-4 and C5-6). Age, sagittal cervical canal diameter, cervical intervertebral disc degeneration, cervical cord compression, and cervical mobilities were evaluated for each group. Group B showed a narrow cervical spinal canal structure at the C3 to C4 pedicle levels, while groups C and D showed narrow structures at the C4 to C6 pedicle levels in the cervical spine. Additionally, the sagittal cervical canal diameters at all pedicle levels, except C7, in group D were significantly smaller than those observed in group C. We demonstrated the differences in the pathogenetic processes for the development of cervical spinal canal stenosis between C3-4, C5-6, and two-level cervical segments stenosis. Our results suggest that the developmental morphological structure of the cervical spinal canal plays an important role in the development of cervical canal stenosis at different segments. Moreover, individuals with sagittal cervical canal diameters of less than 13 mm may be exposed to an increased risk for future development of cervical spinal canal stenosis at the upper cervical segments following stenosis at the lower cervical segments.
EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis

We have developed a toolbox and graphic user interface, EEGLAB, running under the crossplatform MATLAB environment (The Mathworks, Inc.) for processing collections of single-trial and/or averaged EEG data of any number of channels. Available functions include EEG data, channel and event information importing, data visualization (scrolling, scalp map and dipole model plotting, plus multi-trial ERP-image plots), preprocessing (including artifact rejection, filtering, epoch selection, and averaging), independent component analysis (ICA) and time/frequency decompositions including channel and component cross-coherence supported by bootstrap statistical methods based on data resampling. EEGLAB functions are organized into three layers. Top-layer functions allow users to interact with the data through the graphic interface without needing to use MATLAB syntax. Menu options allow users to tune the behavior of EEGLAB to available memory. Middle-layer functions allow users to customize data processing using command history and interactive 'pop' functions. Experienced MATLAB users can use EEGLAB data structures and stand-alone signal processing functions to write custom and/or batch analysis scripts. Extensive function help and tutorial information are included. A 'plug-in' facility allows easy incorporation of new EEG modules into the main menu. EEGLAB is freely available (http://www.sccn.ucsd.edu/eeglab/) under the GNU public license for noncommercial use and open source development, together with sample data, user tutorial and extensive documentation.
First-trimester screening for trisomy 21 using alpha-fetoprotein.

OBJECTIVE
To investigate the potential value of adding maternal serum alpha-fetoprotein (AFP) to free β-human chorionic gonadotropin (β-hCG) and PAPP-A and fetal nuchal translucency (NT) thickness in first-trimester screening for trisomy 21.


METHODS
In this case control study, serum AFP was measured in 100 trisomy 21 and 1,500 euploid pregnancies in which screening for trisomy 21 had been performed by a combination of serum free β-hCG and PAPP-A and fetal NT at 11-13 weeks' gestation. We examined the effect of adding AFP on the performance of screening by the combined test.


RESULTS
In the trisomy 21 pregnancies, the median multiple of the normal median AFP, adjusted for gestational age, maternal weight, racial origin, smoking status and method of conception, was significantly reduced (0.7037, 95% CI: 0.6398-0.7739). Adding AFP to the combined test improved the performance of screening and for a risk cut-off of 1 in 100, the false-positive rate was reduced from 2.8 by 0.4% (95% CI: 0.13-0.77%) without a significant change in detection rate.


CONCLUSIONS
Inclusion of serum AFP improves the performance of the first-trimester combined test in screening for trisomy 21.
Within-trial economic evaluation of diabetes-specific cognitive behaviour therapy in patients with type 2 diabetes and subthreshold depression

BACKGROUND
Despite the high prevalence of subthreshold depression in patients with type 2 diabetes, evidence on cost-effectiveness of different therapy options for these patients is currently lacking.


METHODS/DESIGN
Within-trial economic evaluation of the diabetes-specific cognitive behaviour therapy for subthreshold depression. Patients with diabetes and subthreshold depression are randomly assigned to either 2 weeks of diabetes-specific cognitive behaviour group therapy (n = 104) or to standard diabetes education programme only (n = 104). Patients are followed for 12 months. During this period data on total health sector costs, patient costs and societal productivity costs are collected in addition to clinical data. Health related quality of life (the SF-36 and the EQ-5D) is measured at baseline, immediately after the intervention, at 6 and at 12 months after the intervention. Quality adjusted life years (QALYs), and cumulative costs will be estimated for each arm of the trial. Cost-effectiveness of the diabetes-specific cognitive behaviour group therapy will be analysed from the perspective of the German statutory health insurance and from the societal perspective. To this end, incremental cost-effectiveness ratio (ICER) in terms of cost per QALY gained will be calculated.


DISCUSSION
Some methodological issues of the described economic evaluation are discussed.


TRIAL REGISTRATION
The trial has been registered at the Clinical Trials Register (NCT01009138).
Quantitative Analysis of Intrusion Detection Systems : Snort and Suricata

Any modern organization that is serious about security deploys a network intrusion detection system (NIDS) to monitor network traffic for signs of malicious activity. The most widely deployed NIDS system is Snort, an open source system originally released in 1998. Snort is a single threaded system that uses a set of clear text rules to instruct a base engine how to react when particular traffic patterns are detected. In 2009, the US Department of Homeland Security and a consortium of private companies provided substantial grant funding to a newly created organization known as the Open Information Security Foundation (OISF), to build a multi-threaded alternative to Snort, called Suricata. Despite many similarities between Snort and Suricata, the OISF stated it was essential to replace the older single-threaded Snort engine with a multi-threaded system that could deliver higher performance and better scalability. Key Snort developers argued that Suricata’s multi-threaded architecture would actually slow the detection process. Given these competing claims, an objective head-to-head comparison of the performance of Snort and Suricata is needed. In this paper, we present a comprehensive quantitative comparison of the two systems. We have developed a rigorous testing framework that examines the performance of both systems as we scale system resources. Our results show that a single instance of Suricata is able to deliver substantially higher performance than a corresponding single instance of Snort, but has problems scaling with a higher number of cores. We find that while Suricata needs tuning for a higher number of cores, it is still able to surpass Snort even at 1 core where we would have expected Snort to shine.
Hidradenitis Suppurativa in Children Treated with Finasteride-A Case Series.

BACKGROUND
Hidradenitis suppurativa (HS) is rare in childhood, with only 2% of cases in patients younger than 11 years. It is a chronic, recurrent, debilitating condition for which no universally effective treatment has been developed. We present five cases of children with HS diagnosed between the ages of 6 and 11 years.


METHODS
Patients were treated with oral finasteride 1 to 5 mg/day. All had entered puberty at the time of treatment initiation. All had normal laboratory results before starting treatment. The maximum duration of treatment was 24 months.


RESULTS
Four patients were female. Two were overweight. Three had been previously treated with oral antibiotics, and two of these with oral isotretinoin, with partial or no improvement. Overall improvement of the disease was observed in all patients, with a reduction of the frequency and intensity of the flares. No adverse effects were observed or reported during treatment.


CONCLUSION
Treatment of HS can be challenging. The options available include antimicrobials, immunosuppressants, hormonal therapies, lasers, and surgery. The authors report the largest series of children with HS treated with finasteride. The results support the use of finasteride as monotherapy for the treatment of this disease in children. Further studies are necessary to fully understand the role of this drug in the management of this disease.
A 24-week comparison of low-dose ciclesonide and fluticasone propionate in mild to moderate asthma.

OBJECTIVE
To compare the efficacy of ciclesonide (80 microg/day) with fluticasone propionate (200 microg/day) in mild to moderate persistent asthma.


METHODS
Patients aged 12-75 years and previously treated with low doses of inhaled corticosteroid (fluticasone propionate 250 microg/day or equivalent) entered a 2-4 week run-in period during which only rescue medication was permitted. For inclusion into the double-blind, 24-week treatment period, patients had to show a forced expiratory volume in 1s (FEV(1)) of 61-90% predicted and a decrease in FEV(1) during run-in of >or=10%. Patients (n = 480) were randomized to ciclesonide 80 microg (ex-actuator) once daily in the evening or fluticasone propionate 100 microg (ex-valve) twice daily. The primary efficacy variable was the change from baseline in FEV(1). Secondary efficacy variables included asthma control and asthma-specific quality of life.


RESULTS
Both treatments significantly increased FEV(1) and other lung function variables from baseline (p < 0.0001, both groups, all variables). The least squares mean increases in FEV(1) were 0.46L (ciclesonide) and 0.52L (fluticasone propionate); non-inferiority of ciclesonide to fluticasone propionate was demonstrated (p = 0.0002, per-protocol analysis). Five patients in each group experienced asthma exacerbations. Improvements in the percent of days with asthma control (days with no asthma symptoms and no use of rescue medication) and asthma-specific quality of life were comparable between treatments.


CONCLUSIONS
The study confirmed similar efficacy of ciclesonide 80 microg once daily and fluticasone propionate 100 microg twice daily in mild to moderate persistent asthma. The low dose of ciclesonide was efficacious during long-term treatment. EudraCT number: 2004-001072-39.
Green synthesis and characterization of silver nanoparticles using alcoholic flower extract of Nyctanthes arbortristis and in vitro investigation of their antibacterial and cytotoxic activities.

Here we report the synthesis of silver nanoparticles using ethanolic flower extract of Nyctanthes arbortristis, UVvisible spectra and TEM indicated the successful formation of silver nanoparticles. Crystalline nature of the silver nanoparticles was confirmed by X-ray diffraction. Fourier Transform Infra-Red Spectroscopy analysis established the capping of the synthesized silver nanoparticles with phytochemicals naturally occurring in the ethanolic flower extract of N. arbortristis. The synthesized silver nanoparticles showed antibacterial activity against the pathogenic strain of Escherichia coli MTCC 443. Furthermore, cytotoxicity of the silver nanoparticles was tested on mouse fibroblastic cell line (L929) and found to be non-toxic, which thus proved their biocompatibility. Antibacterial activity and cytotoxicity assay carried out in this study open up an important perspective of the synthesized silver nanoparticles.
The clinical findings in young adults with acute scrotal pain.

BACKGROUND
Acute scrotal pain (ASP) is a common symptom of young adults. Testicular torsion is the most important diagnosis in these cases. It is a medical emergency in which the diagnosis must be made rapidly to prevent testicular loss. This requires a high index of clinical suspicion and prompt surgical intervention. This study was conducted to examine the spectrum of diagnoses in young man with ASP in a prehospital setting, the frequency of significant diagnoses, and their outcomes.


METHODS
The medical records of young adults in their obligatory military service presenting with ASP to primary care clinics from 2004 to 2014 were reviewed using the keywords: pain, testis, torsion, and orchialgia. Anamnestic data, physical findings, primary care physician decisions, and final outcomes were analyzed.


RESULTS
A total of 9922 medical visits were recorded. Idiopathic scrotal pain, varicocele, scrotal trauma, and genital tract infections were the most common diagnoses. In 3 visits (0.03%), testicular cancer was diagnosed. Testicular torsion was the etiology of ASP in only 12 (0.12%) visits, and 60% the testes were salvaged. The mean duration of symptoms in the salvaged group was 6.33 hours; and in the nonsalvaged group, 44 hours.


CONCLUSIONS
Testicular torsion is the etiology of ASP in only 0.12% of the visits to the primary care clinic. Patient delay before attending the primary care is responsible for most of the testes lost. Patient education in addition to high index of suspicion of primary care physicians is needed for salvage of more testicles.