LLukas22/scidocs huggingface dataset:
Ten Simple Rules for Developing Usable Software in Computational Biology

The rise of high-throughput technologies in molecular biology has led to a massive amount of publicly available data. While computational method development has been a cornerstone of biomedical research for decades, the rapid technological progress in the wet lab makes it difficult for software development to keep pace. Wet lab scientists rely heavily on computational methods, especially since more research is now performed in silico. However, suitable tools do not always exist, and not everyone has the skills to write complex software. Computational biologists are required to close this gap, but they often lack formal training in software engineering. To alleviate this, several related challenges have been previously addressed in the Ten Simple Rules series, including reproducibility [1], effectiveness [2], and open-source development of software [3, 4]. Here, we want to shed light on issues concerning software usability. Usability is commonly defined as “a measure of interface quality that refers to the effectiveness, efficiency, and satisfaction with which users can perform tasks with a tool” [5]. Considering the subjective nature of this topic, a broad consensus may be hard to achieve. Nevertheless, good usability is imperative for achieving wide acceptance of a software tool in the community. In many cases, academic software starts out as a prototype that solves one specific task and is not geared for a larger user group. As soon as the developer realizes that the complexity of the problems solved by the software could make it widely applicable, the software will grow to meet the new demands. At least by this point, if not sooner, usability should become a priority. Unfortunately, efforts in scientific software development are constrained by limited funding, time, and rapid turnover of group members. As a result, scientific software is often poorly documented, non-intuitive, non-robust with regards to input data and parameters, and hard to install. For many use cases, there is a plethora of tools that appear very similar and make it difficult for the user to select the one that best fits their needs. Not surprisingly, a substantial fraction of these tools are probably abandonware; i.e., these are no longer actively developed or supported in spite of their potential value to the scientific community. To our knowledge, software development as part of scientific research is usually carried out by individuals or small teams with no more than two or three members. Hence, the responsibility of designing, implementing, testing, and documenting the code rests on few shoulders. Additionally, there is pressure to produce publishable results or, at least, to contribute analysis work to ongoing projects. Consequently, academic software is typically released as a prototype. We acknowledge that such a tool cannot adhere to and should not be judged by the standards
USING JTAG BASED ON HOL / SCALA / LMS / JIKESRVM / JVM INFORMATICS FRAMEWORK – AN INSIGHT INTO FORENSIC IMAGING OF EMBEDDED SYSTEMS IN THE CONTEXT OF SMART DEVICES

In this technical note the author is interested in exploiting the advantages of Higher Order Logic(HOL),Scala,JVM,JikesRVM & LMS in the IoT scenario.The title is highly self explanatory hence detailed explanation is skipped. index words: IoT/JVM/Scala/HOL/LMS(Lightweight Modular Staging)/Forensic Imaging/Firmware/JTAG. Introduction & Inspiration : [i] “JTAG Explained (finally!): Why "IoT", Software Security Engineers, and Manufacturers Should Care “ Source : http://blog.senr.io/blog/jtag-explained [ii] Forensic imaging of embedded systems using JTAG (boundary-scan) https://doi.org/10.1016/j.diin.2006.01.003 [iii] Scala Based FPGA Design Flow (Abstract Only) https://doi.org/10.1145/3020078.3021762 Informatics Framework Implementation : Figure I – Approximate Informatics Framework – HOL/Scala/JTAG/JikesRVM/LMS/IoT ** Readers please note “the actual implementation might vary to some extent”. Analysis of the Informatics Framework: Informatics framework was explored based on HOL/Scala/JTAG/JVM/IoT to perform forensic imaging of embedded systems in the context of Smart Devices.[Refs from 1 to 9 are used ].Figure I illustrates the main idea to help those who are interested in this interesting domain of embedded systems. Conclusion/s with future perspectives : A simple HOL/Scala/LMS/JVM/IoT based “Informatics Framework” was designed and presented in this technical note.It is sincerely hoped that many new comers in this promising area will explore this challenging domain of “Forensic Imaging of Embedded Systems” using JTAG. Additional Information on Software Used : [a] https://isabelle.in.tum.de/ HOL [b] https://www.isa-afp.org/entries/AWN.html HOL based Wireless Library [c] http://www.scala-lang.org/ Scala Programming Language. [d] http://scala-lms.github.io/ Lightweight Modular Staging (LMS) is a runtime code generation approach. [e] http://www.spiral.net/software/spiral-scala.html Spiral for DSP based in Scala. [f] http://www.jikesrvm.org/ Java Virtual Machine. [g] https://xdk.bosch-connectivity.com/ IoT Environment. [h] https://wilsonmar.github.io/intel-iot-setup/ IoT Environment.
On an Arithmetic Inequality

We obtain an arithmetic proof and a refinement of the inequality φ(n) + σk(n) < 2n , where n ≥ 2 and k ≥ 2. An application to another inequality is also provided.
Low-Temperature Two-Phase Microchannel Cooling for High-Heat-Flux Thermal Management of Defense Electronics

For a given heat sink thermal resistance and ambient temperature, the temperature of an electronic device rises fairly linearly with increasing device heat flux. This relationship is especially problematic for defense electronics, where heat dissipation is projected to exceed 1000 W/cm2 in the near future. Direct and indirect low-temperature refrigeration cooling facilitate appreciable reduction in the temperature of both coolant and device. This paper explores the benefits of cooling the device using direct and indirect refrigeration cooling systems. In the direct cooling system, a microchannel heat sink serves as an evaporator in a conventional vapor compression cycle using R134a as working fluid. In the indirect cooling system, HFE 7100 is used to cool the heat sink in a primary pumped liquid loop that rejects heat to a secondary refrigeration loop. Two drastically different flow behaviors are observed in these systems. Because of compressor performance constraints, mostly high void fraction two-phase patterns are encountered in the R134a system, dominated by saturated boiling. On the other hand, the indirect refrigeration cooling system facilitates highly subcooled boiling inside the heat sink. Both systems are shown to provide important cooling benefits, but the indirect cooling system is far more effective at dissipating high heat fluxes. Tests with this system yielded cooling heat fluxes as high as 840 W/cm2 without incurring critical heat flux (CHF). Results from both systems are combined to construct an overall map of performance trends relative to mass velocity, subcooling, pressure, and surface tension. Extreme conditions of near-saturated flow, low mass velocity, and low pressure produce ldquomicrordquo behavior, where macrochannel flow pattern maps simply fail to apply, instabilities are prominent, and CHF is quite low. One the other hand, systems with high mass velocity, high subcooling, and high pressure are far more stable and yield very high CHF values; two-phase flow in these systems follows the fluid flow and heat transfer behavior as well as the flow pattern maps of macrochannels.
Large Scale Labelled Video Data Augmentation for Semantic Segmentation in Driving Scenarios

In this paper we present an analysis of the effect of large scale video data augmentation for semantic segmentation in driving scenarios. Our work is motivated by a strong correlation between the high performance of most recent deep learning based methods and the availability of large volumes of ground truth labels. To generate additional labelled data, we make use of an occlusion-aware and uncertainty-enabled label propagation algorithm [8]. As a result we increase the availability of high-resolution labelled frames by a factor of 20, yielding in a 6.8% to 10.8% rise in average classification accuracy and/or IoU scores for several semantic segmentation networks. Our key contributions include: (a) augmented CityScapes and CamVid datasets providing 56.2K and 6.5K additional labelled frames of object classes respectively, (b) detailed empirical analysis of the effect of the use of augmented data as well as (c) extension of proposed framework to instance segmentation.
Delayed sodium 18F-fluoride PET/CT imaging does not improve quantification of vascular calcification metabolism: results from the CAMONA study.

BACKGROUND
This study aimed to determine if delayed sodium (18)F-fluoride (Na(18)F) PET/CT imaging improves quantification of vascular calcification metabolism. Blood-pool activity can disturb the arterial Na(18)F signal. With time, blood-pool activity declines. Therefore, delayed imaging can potentially improve quantification of vascular calcification metabolism.


METHODS AND RESULTS
Twenty healthy volunteers and 18 patients with chest pain were prospectively assessed by triple time-point PET/CT imaging at approximately 45, 90, and 180 minutes after Na(18)F administration. For each time point, global uptake of Na(18)F was determined in the coronary arteries and thoracic aorta by calculating the blood-pool-corrected maximum standardized uptake value (cSUV(MAX)). A target-to-background ratio (TBR) was calculated to determine the contrast resolution at 45, 90, and 180 minutes. Furthermore, we assessed whether the acquisition time-point affected the relation between cSUV(MAX) and the estimated 10-year risk for fatal cardiovascular disease (SCORE %). Coronary cSUV(MAX) (P = .533) and aortic cSUV(MAX) (P = .654) remained similar with time, whereas the coronary TBR (P < .0001) and aortic TBR (P < .0001) significantly increased with time. Even though the contrast resolution improved with time, positive correlations between SCORE % and coronary cSUV(MAX) (P < .020) and aortic cSUV(MAX) (P < .005) were observed at all investigated time points.


CONCLUSIONS
Delayed Na(18)F PET/CT imaging does not improve quantification of vascular calcification metabolism. Although contrast resolution improves with time, arterial Na(18)F avidity is invariant to the time between Na(18)F administration and PET/CT acquisition. Therefore, the optimal PET/CT acquisition time-point to quantify vascular calcification metabolism is achieved as early as 45 minutes after Na(18)F administration.
Prospective study on the association between diet quality and depression in mid-aged women over 9 years.

PURPOSE
To examine the longitudinal association between diet quality and depression using prospective data from the Australian Longitudinal Study on Women's Health.


METHODS
Women born in 1946-1951 (n = 7877) were followed over 9 years starting from 2001. Dietary intake was assessed using the Dietary Questionnaire for Epidemiological Studies (version 2) in 2001 and a shortened form in 2007 and 2010. Diet quality was summarised using the Australian Recommended Food Score. Depression was measured using the 10-item Centre for Epidemiologic Depression Scale and self-reported physician diagnosis. Pooled logistic regression models including time-varying covariates were used to examine associations between diet quality tertiles and depression. Women were also categorised based on changes in diet quality during 2001-2007. Analyses were adjusted for potential confounders.


RESULTS
The highest tertile of diet quality was associated marginally with lower odds of depression (OR 0.94; 95 % CI 0.83, 1.00; P = 0.049) although no significant linear trend was observed across tertiles (OR 1.00; 95 % CI 0.94, 1.10; P = 0.48). Women who maintained a moderate or high score over 6 years had a 6-14 % reduced odds of depression compared with women who maintained a low score (moderate vs low score-OR 0.94; 95 % CI 0.80, 0.99; P = 0.045; high vs low score-OR 0.86; 95 % CI 0.77, 0.96; P = 0.01). Similar results were observed in analyses excluding women with prior history of depression.


CONCLUSION
Long-term maintenance of good diet quality may be associated with reduced odds of depression. Randomised controlled trials are needed to eliminate the possibility of residual confounding.
Follow-up after transanal endoscopic microsurgery or transanal excision of large benign rectal polyps

Methods: Between January 1986 and December 1995, 238 patients with benign rectal polyps under-went either transanal endoscopic microsurgery (n = 226) or transanal excision (n = 12) at the Clinic of General and Abdominal Surgery, Johannes Gutenberg-University, Mainz. Results: Mean polyp size was 4.2 cm; 89.1% of polyps measured more than 2 cm in diameter. In 89.1% of cases, histological analysis revealed polyps containing tubulovillous or villous adenomas. Synchronous colonic polyps were detected in 12.5% of patients. Follow-up data are available on 222 patients (94%). At follow-up examination, 169 of the 193 surviving patients (87.6%) were recurrence free. Seven of 193 patients (3.6%) had developed neoplastic colonic polyps and, in 17 patients (8.8%), metachronous polyps were detected. Conclusions: Transanal endoscopic microsurgical polypectomy was furthermore demonstrated to be a low-risk procedure with a low recurrence rate for the complete resection of large rectal polyps. At a follow-up rate of 61.1%, the incidence of metachronous carcinoma ranged at 3.1%, which is markedly below the rate of 8–18% for tubulovillous or villous adenomas larger than 1 cm in diameter cited in the literature.
The effect of walnut intake on factors related to prostate and vascular health in older men

BACKGROUND
Tocopherols may protect against prostate cancer and cardiovascular disease (CVD).


METHODS
We assessed the effect of walnuts, which are rich in tocopherols, on markers of prostate and vascular health in men at risk for prostate cancer. We conducted an 8-week walnut supplement study to examine effects of walnuts on serum tocopherols and prostate specific antigen (PSA). Subjects (n = 21) consumed (in random order) their usual diet +/- a walnut supplement (75 g/d) that was isocalorically incorporated in their habitual diets. Prior to the supplement study, 5 fasted subjects participated in an acute timecourse experiment and had blood taken at baseline and 1, 2, 4, and 8 h after consuming walnuts (75 g).


RESULTS
During the timecourse experiment, triglycerides peaked at 4 h, and gamma-tocopherol (gamma-T) increased from 4 to 8 h. Triglyceride - normalized gamma-T was two-fold higher (P = 0.01) after 8 versus 4 h. In the supplement study, change from baseline was +0.83 +/- 0.52 micromol/L for gamma-T, -2.65 +/- 1.30 micromol/L for alpha-tocopherol (alpha-T) and -3.49 +/- 1.99 for the tocopherol ratio (alpha-T: gamma-T). A linear mixed model showed that, although PSA did not change, the ratio of free PSA:total PSA increased and approached significance (P = 0.07). The alpha-T: gamma-T ratio decreased significantly (P = 0.01), partly reflecting an increase in serum gamma-T, which approached significance (P = 0.08).


CONCLUSION
The significant decrease in the alpha-T: gamma-T ratio with an increase in serum gamma-T and a trend towards an increase in the ratio of free PSA:total PSA following the 8-week supplement study suggest that walnuts may improve biomarkers of prostate and vascular status.
Analysing Political Discourse : Toward a Cognitive Approach 1

The critical study of political discourse has up until very recently rested solely within the domain of the social sciences. Working within a linguistics framework, Critical Discourse Analysis (CDA), in particular Fairclough (Fairclough 1989, 1995a, 1995b, 2001; Fairclough and Wodak 1997), has been heavily influenced by Foucault. 2 The linguistic theory that CDA and critical linguistics especially (which CDA subsumes) has traditionally drawn upon is Halliday‟s Systemic-Functional Grammar, which is largely concerned with the function of language in the social structure 3 (Fowler et al. 1979; Fowler 1991; Kress and Hodge 1979).
Linking GIS and water resources management models: an object-oriented method

Many challenges are associated with the integration of geographic information systems (GISs) with models in specific applications. One of them is adapting models to the environment of GISs. Unique aspects of water resource management problems require a special approach to development of GIS data structures. Expanded development of GIS applications for handling water resources management analysis can be assisted by use of an object oriented approach. In this paper, we model a river basin water allocation problem as a collection of spatial and thematic objects. A conceptual GIS data model is formulated to integrate the physical and logical components of the modeling problem into an operational framework, based on which, extended GIS functions are developed to implement a tight linkage between the GIS and the water resources management model. Through the object-oriented approach, data, models and users interfaces are integrated in the GIS environment, creating great flexibility for modeling and analysis. The concept and methodology described in this paper is also applicable to connecting GIS with models in other fields that have a spatial dimension and hence to which GIS can provide a powerful additional component of the modeler’s tool kit.  2002 Elsevier Science Ltd. All rights reserved.
Working memory, psychiatric symptoms, and academic performance at school

Previous studies of the relationship among working memory function, academic performance, and behavior in children have focused mainly on clinical populations. In the present study, the associations of the performance in audio- and visuospatial working memory tasks to teacher reported academic achievement and psychiatric symptoms were evaluated in a sample of fifty-five 6-13-year-old school children. Working memory function was measured by visual and auditory n-back tasks. Information on incorrect responses, reaction times, and multiple and missed responses were collected during the tasks. The children's academic performance and behavioral and emotional status were evaluated by the Teacher Report Form. The results showed that good spatial working memory performance was associated with academic success at school. Children with low working memory performance, especially audiospatial memory, were reported to have more academic and attentional/behavioral difficulties at school than children with good working memory performance. An increased number of multiple and missed responses in the auditory and visual tasks was associated with teacher reported attentional/behavioral problems and in visual tasks with teacher reported anxiety/depressive symptoms. The results suggest that working memory deficits may underlie some learning difficulties and behavioral problems related to impulsivity, difficulties in concentration, and hyperactivity. On the other hand, it is possible that anxiety/depressive symptoms affect working memory function, as well as the ability to concentrate, leading to a lower level of academic performance at school.
Protective immunity of E. coli-synthesized NS1 protein of Japanese encephalitis virus

Immunogenicity and protective efficacy of recombinant Japanese encephalitis virus (JEV) NS1 proteins generated using DNA vaccines and recombinant viruses have been demonstrated to induce protection in mice against a challenge of JEV at a lethal dose. The West Nile virus NS1 region expressed in E. coli is recognized by these protective monoclonal antibodies and, in this study, we compare immunogenicity and protective immunity of the E. coli-synthesized NS1 protein with another protective immunogen, the envelope domain III (ED3). Pre-challenge, detectable titers of JEV-specific neutralizing antibody were detected in the immunized mice with E. coli-synthesized ED3 protein (PRNT50 = 1:28) and the attenuated JEV strain T1P1 (PRNT50 = 1:53), but neutralizing antibodies were undetectable in the immunized mice with E. coli-synthesized NS1 protein (PRNT50 < 1:10). However, the survival rate of the NS1-immunized mice against the JEV challenge was 87.5% (7/8), showing significantly higher levels of protection than the ED3-immunized mice, 62.5% (5/8) (P = 0.041). In addition, E. coli-synthesized NS1 protein induced a significant increase of anti-NS1 IgG1 antibodies, resulting in an ELISA titer of 100,1000 in the immunized sera before lethal JEV challenge. Surviving mice challenged with the virulent JEV strain Beijing-1 showed a ten-fold or greater rise in IgG1 and IgG2b titers of anti-NS1 antibodies, implying that the Th2 cell activation might be predominantly responsible for antibody responses and mice protection.
Attitudes and actions of asthma patients on regular maintenance therapy: the INSPIRE study

BACKGROUND
This study examined the attitudes and actions of 3415 physician-recruited adults aged > or = 16 years with asthma in eleven countries who were prescribed regular maintenance therapy with inhaled corticosteroids or inhaled corticosteroids plus long-acting beta2-agonists.


METHODS
Structured interviews were conducted to assess medication use, asthma control, and patients' ability to recognise and self-manage worsening asthma.


RESULTS
Despite being prescribed regular maintenance therapy, 74% of patients used short-acting beta2-agonists daily and 51% were classified by the Asthma Control Questionnaire as having uncontrolled asthma. Even patients with well-controlled asthma reported an average of 6 worsenings/year. The mean period from the onset to the peak symptoms of a worsening was 5.1 days. Although most patients recognised the early signs of worsenings, the most common response was to increase short-acting beta2-agonist use; inhaled corticosteroids were increased to a lesser extent at the peak of a worsening.


CONCLUSION
Previous studies of this nature have also reported considerable patient morbidity, but in those studies approximately three-quarters of patients were not receiving regular maintenance therapy and not all had a physician-confirmed diagnosis of asthma. This study shows that patients with asthma receiving regular maintenance therapy still have high levels of inadequately controlled asthma. The study also shows that patients recognise deteriorating asthma control and adjust their medication during episodes of worsening. However, they often adjust treatment in an inappropriate manner, which represents a window of missed opportunity.