LLukas22/scidocs huggingface dataset:
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords

Due to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manually or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the growing volume of bioinformatics datasets, emerging new software tools and approaches motivates new solutions. To provide a new tool for these current cases, I present the Biobtree bioinformatics tool. Biobtree effectively fetches and indexes identifiers and special keywords with their related identifiers from supported datasets, optionally with user pre-defined datasets and provides a web interface, web services and direct B+ tree data structure based single uniform database output. Biobtree can handle billions of identifiers and runs via a single executable file with no installation and dependency required. It also aims to provide a relatively small codebase for easy maintenance, addition of new features and extension to larger datasets. Biobtree is available to download from . GitHub
Integrated assessment of policy interventions for promoting sustainable irrigation in semi-arid environments: a hydro-economic modeling approach.

Sustaining irrigated agriculture to meet food production needs while maintaining aquatic ecosystems is at the heart of many policy debates in various parts of the world, especially in arid and semi-arid areas. Researchers and practitioners are increasingly calling for integrated approaches, and policy-makers are progressively supporting the inclusion of ecological and social aspects in water management programs. This paper contributes to this policy debate by providing an integrated economic-hydrologic modeling framework that captures the socio-economic and environmental effects of various policy initiatives and climate variability. This modeling integration includes a risk-based economic optimization model and a hydrologic water management simulation model that have been specified for the Middle Guadiana basin, a vulnerable drought-prone agro-ecological area with highly regulated river systems in southwest Spain. Namely, two key water policy interventions were investigated: the implementation of minimum environmental flows (supported by the European Water Framework Directive, EU WFD), and a reduction in the legal amount of water delivered for irrigation (planned measure included in the new Guadiana River Basin Management Plan, GRBMP, still under discussion). Results indicate that current patterns of excessive water use for irrigation in the basin may put environmental flow demands at risk, jeopardizing the WFD's goal of restoring the 'good ecological status' of water bodies by 2015. Conflicts between environmental and agricultural water uses will be stressed during prolonged dry episodes, and particularly in summer low-flow periods, when there is an important increase of crop irrigation water requirements. Securing minimum stream flows would entail a substantial reduction in irrigation water use for rice cultivation, which might affect the profitability and economic viability of small rice-growing farms located upstream in the river. The new GRBMP could contribute to balance competing water demands in the basin and to increase economic water productivity, but might not be sufficient to ensure the provision of environmental flows as required by the WFD. A thoroughly revision of the basin's water use concession system for irrigation seems to be needed in order to bring the GRBMP in line with the WFD objectives. Furthermore, the study illustrates that social, economic, institutional, and technological factors, in addition to bio-physical conditions, are important issues to be considered for designing and developing water management strategies. The research initiative presented in this paper demonstrates that hydro-economic models can explicitly integrate all these issues, constituting a valuable tool that could assist policy makers for implementing sustainable irrigation policies.
2 A 28 GHz 32-Element Phased-Array Transceiver IC with Concurrent Dual Polarized Beams and 1 . 4 Degree Beam-Steering Resolution for 5 G Communication

Next-generation mobile technology (5G) aims to provide an improved experience through higher data-rates, lower latency, and improved link robustness. Millimeter-wave phased arrays offer a path to support multiple users at high datarates using high-bandwidth directional links between the base station and mobile devices. To realize this vision, a phased-array-based pico-cell must support a large number of precisely controlled beams, yet be compact and power efficient. These system goals have significant mm-wave radio interface implications, including scalability of the RFIC+antenna-array solution, increase in the number of concurrent beams by supporting dual polarization, precise beam steering, and high output power without sacrificing TX power efficiency. Packaged Si-based phased arrays [1-3] with nonconcurrent dual-polarized TX and RX operation [2,3], concurrent dual-polarized RX operation [3] and multi-IC scaling [3,4] have been demonstrated. However, support for concurrent dual-polarized operation in both RX and TX remains unaddressed, and high output power comes at the cost of power consumption, cooling complexity and increased size. The RFIC reported here addresses these challenges. It supports concurrent and independent dualpolarized operation in TX and RX modes, and is compatible with a volume-efficient, scaled, antenna-in-package array. A new TX/RX switch at the shared antenna interface enables high output power without sacrificing TX efficiency, and a t-line-based phase shifter achieves <1° RMS error and <5° phase steps for precise beam control.
CoQA: A Conversational Question Answering Challenge

Humans gather information by engaging in conversations involving a series of interconnected questions and answers. For machines to assist in information gathering, it is therefore essential to enable them to answer conversational questions. We introduce CoQA, a novel dataset for building Conversational Question Answering systems.1 Our dataset contains 127k questions with answers, obtained from 8k conversations about text passages from seven diverse domains. The questions are conversational, and the answers are free-form text with their corresponding evidence highlighted in the passage. We analyze CoQA in depth and show that conversational questions have challenging phenomena not present in existing reading comprehension datasets, e.g., coreference and pragmatic reasoning. We evaluate strong conversational and reading comprehension models on CoQA. The best system obtains an F1 score of 65.1%, which is 23.7 points behind human performance (88.8%), indicating there is ample room for improvement. We launch CoQA as a challenge to the community at https://stanfordnlp. github.io/coqa/.
The effects of prolonged wear of textured shoe insoles on gait, foot sensation and proprioception in people with multiple sclerosis: study protocol for a randomised controlled trial

BACKGROUND
Many people with multiple sclerosis experience problems with walking, which can make daily activities difficult and often leads to falls. Foot sensation plays an important role in keeping the body balanced whilst walking; however, people with multiple sclerosis often have poor sensation on the soles of their feet. Wearing a specially designed shoe insole, which enhances plantar sensory information, could help people with multiple sclerosis to walk better. This study will explore whether long-term wear of a textured insole can improve walking in people with multiple sclerosis.


METHODS
A prospective randomised controlled trial with two parallel groups will be conducted aiming to recruit 176 people with multiple sclerosis living in the community (Brisbane, Australia). Adults with a clinical diagnosis of multiple sclerosis, Disease Steps score 1-4, who are ambulant over 100 m and who meet specific inclusion criteria will be recruited. Participants will be randomised to a smooth control insole (n = 88) or textured insole (n = 88) group. The allocated insole will be worn for 12-weeks within participants' own footwear, with self-report wear diaries and falls calendars being completed over this period. Blinded assessors will conduct two baseline assessments and one post-intervention assessment. Gait tasks will be completed barefoot, wearing standardised footwear only, and wearing standardised footwear with smooth and textured insoles. The primary outcome measure will be mediolateral base of support when walking over even and uneven surfaces. Secondary measures include spatiotemporal gait parameters (stride length, stride time variability, double-limb support time, velocity), gait kinematics (hip, knee, and ankle joint angles, toe clearance, trunk inclination, arm swing, mediolateral pelvis/head displacement), foot sensation (light touch-pressure, vibration, two-point discrimination) and proprioception (ankle joint position sense). Group allocation will be concealed and all analyses will be based on an intention-to-treat principle.


DISCUSSION
This study will explore the effects of wearing textured insoles over 12-weeks on gait, foot sensation and proprioception in people with multiple sclerosis. The study has the potential to identify a new, evidence-based footwear intervention which has the capacity to enhance mobility and independent living in people with multiple sclerosis.


TRIAL REGISTRATION
Australian New Zealand Clinical Trials Registry ACTRN12615000421538 . Registered 4 May 2015.
Efficacy of acamprosate for alcohol dependence in a family medicine setting in the United States: a randomized, double-blind, placebo-controlled study.

BACKGROUND
Acamprosate has been found to enhance rates of complete abstinence and to increase percent days abstinent (PDA) from alcohol relative to placebo treatment. As most U.S. clinical trials of acamprosate have been conducted in alcohol and other drug specialty clinics, there is a need to examine the efficacy of acamprosate in generalist settings. This study tested the efficacy of acamprosate versus placebo on the primary study outcome of PDA in the treatment of alcohol-dependent patients in a family medicine setting. Secondary study outcomes included percent heavy drinking days (%HDD) and gamma glutamyltransferase level (normal or high).


METHODS
A randomized, double-blind, placebo-controlled, parallel group design of acamprosate was conducted in 2 family medicine settings (North Carolina and Wisconsin). One hundred volunteers were recruited primarily by advertisement, and participants were assigned to 666 mg (2 pills) oral acamprosate 3 times daily (1,998 mg/d) or matching placebo over a 12-week period. All participants concomitantly received 5 sessions of a brief behavioral intervention from a family/primary care physician.


RESULTS
No significant treatment effect of acamprosate was found on PDA or the secondary outcomes. Significant treatment goal by time interaction effects was found on PDA and %HDD. Participants who had an initial goal of abstinence versus a reduction in alcohol use improved on average over time in PDA and had less %HDD from baseline to the end of treatment.


CONCLUSIONS
This clinical trial did not find evidence of efficacy for acamprosate compared to placebo among alcohol-dependent individuals recruited primarily by advertisement as studied in a primary care setting. Drinking outcomes significantly improved regardless of medication condition. A goal of abstinence was significantly associated with improved drinking outcomes, suggesting that alcohol-dependent patients with such a goal may do particularly well with counseling in a family medicine setting.
Vehicle anti-theft tracking system based on Internet of things

As the amount of urban vehicle grows rapidly, vehicle theft has become a shared concern for all citizens. However, present anti-theft systems lack the tracking and monitoring function. The vehicle anti-theft tracking system based on Internet of things is designed in this article, which can provide all-round active service for the owners. This system is controlled by an RFID module to switch on and off. When the car is stolen, the vibration sensors and pyroelectric infrared sensors mounted inside the vehicle are triggered, and GSM module will send the location information obtained by GPS module to the owner's mobile phone, thus owners can check the position of the vehicle with an android software developed by our team. This system uses android mobile phones as mobile terminal, which is more convenient and flexible than other kinds of like products since the owner can check and track the position of the car immediately with android mobile phone application once the car is stolen.
Platform for Enterprise Privacy Practices: Privacy-Enabled Management of Customer Data

Enterprises collect a large amount of personal data about their customers. Even though enterprises promise privacy to their customers using privacy statements or P3P, there is no methodology to enforce these promises throughout and across multiple enterprises. This article describes the Platform for Enterprise Privacy Practices (E-P3P), which defines technology for privacy-enabled management and exchange of customer data. Its comprehensive privacy-specific access control language expresses restrictions on the access to personal data, possibly shared between multiple enterprises. E-P3P separates the enterprise-specific deployment policy from the privacy policy that covers the complete life cycle of collected data. E-P3P introduces a viable separation of duty between the three “administrators” of a privacy system: The privacy officer designs and deploys privacy policies, the security officer designs access control policies, and the customers can give consent while selecting opt-in and opt-out choices. To appear in2nd Workshop on Privacy Enhancing Technologies , Lecture Notes in Computer Science. Springer Verlag, 2002. Copyright c © Springer
Systemic lupus international collaborating clinics renal activity/response exercise: comparison of agreement in rating renal response.

OBJECTIVE
To assess the degree to which physicians agree with each other and with ratings obtained with 3 existing responder indices, in rating the response to treatment of lupus nephritis.


METHODS
Lupus nephritis patient medical records from 125 pairs of visits (6 months apart) were used to create renal response scenarios. Seven nephrologists and 22 rheumatologists rated each scenario as demonstrating complete response, partial response, same, or worsening. The plurality (most frequent) rating of renal response by the physicians was compared with the calculated score from the renal component of the British Isles Lupus Assessment Group (BILAG) index (original and updated [2004] version) and of the Responder Index for Lupus Erythematosus (RIFLE). The degree of agreement among the physicians was assessed by calculating intraclass correlation coefficients (ICCs). The degree of agreement between the plurality physician rating and ratings obtained with the established response indices was assessed using the kappa statistic.


RESULTS
The ICC among all physicians was 0.64 (0.62 for nephrologists and 0.67 for rheumatologists). The chance-adjusted measure of agreement (kappa coefficient) between the plurality physician rating and the calculated score obtained using established indexes was 0.50 (95% confidence interval [95% CI] 0.38-0.61) for the RIFLE, 0.14 (95% CI 0.03-0.25) for the original BILAG, and 0.23 (95% CI 0.21-0.44) for the BILAG 2004.


CONCLUSION
These findings indicate that rheumatologists as a group and nephrologists as a group have equal agreement in their rating of renal response. There was moderate agreement between plurality physician ratings and ratings obtained using the renal component of the RIFLE. Ratings of response using an index based on the original BILAG did not have good agreement with the plurality physician rating.
Nanoscale origins of the damage tolerance of the high-entropy alloy CrMnFeCoNi

Damage tolerance can be an elusive characteristic of structural materials requiring both high strength and ductility, properties that are often mutually exclusive. High-entropy alloys are of interest in this regard. Specifically, the single-phase CrMnFeCoNi alloy displays tensile strength levels of ∼ 1 GPa, excellent ductility (∼ 60-70%) and exceptional fracture toughness (KJIc>200 MPa√m). Here through the use of in situ straining in an aberration-corrected transmission electron microscope, we report on the salient atomistic to micro-scale mechanisms underlying the origin of these properties. We identify a synergy of multiple deformation mechanisms, rarely achieved in metallic alloys, which generates high strength, work hardening and ductility, including the easy motion of Shockley partials, their interactions to form stacking-fault parallelepipeds, and arrest at planar slip bands of undissociated dislocations. We further show that crack propagation is impeded by twinned, nanoscale bridges that form between the near-tip crack faces and delay fracture by shielding the crack tip.
Random room mobility model and extra-wireless body area network communication in hospital buildings

Wireless body area networks (WBANs) can help in enabling efficient patient monitoring solution for ubiquitous healthcare. Communication in WBANs is undertaken in two phases: intra-WBAN and extra-WBAN. The prevailing WBANs use cellular network or WiFi in the extra-WBAN phase involving communication between the on-body coordinator and access points (APs) connected to the medical server through the internet. The medical applications of the WBANs have stringent requirements of low end-to-end delay and high packet delivery ratio. The authors evaluate the performance of extraWBAN communication in the network of WBANs which is deployed within a building environment. They proposed a mobility model named random room mobility (RRM), which is used to capture the dynamics of WBAN user mobility within the building. They studied the performance of extra-WBAN communication using the proposed mobility model and a random waypoint mobility model. The metrics used in evaluating the performance are packet drop ratio, average node-to-AP delay and average residual energy per node. The authors show that with an increase in the number of WBANs, the traffic generation rate and the payload size have high impact on the packet loss in the network. They studied the performance of extra-WBAN communication using the priority mode available in IEEE 802.11 for provisioning quality-of-service (QoS). We show that it is suitable for medical applications, when the size of network consisting of WBANs, including the QoS-enabled WBANs, is small.
Bone scintigraphy in chronic knee pain: comparison with magnetic resonance imaging.

OBJECTIVE
To compare increased bone uptake of 99Tcm-MDP and magnetic resonance (MR) detected subchondral lesions, osteophytes, and cartilage defects in the knee in middle aged people with long-standing knee pain.


METHODS
Fifty eight people (aged 41-58 years, mean 50) with chronic knee pain, with or without radiographic knee osteoarthritis, were examined with bone scintigraphy. The pattern and the grade of increased bone uptake was assessed. On the same day, a MR examination on a 1.0 T imager was performed. The presence and the grade of subchondral lesions, osteophytes, and cartilage defects were registered.


RESULTS
The kappa values describing the correlation between increased bone uptake and MR detected subchondral lesions varied between 0.79 and 0.49, and between increased bone uptake and MR detected osteophytes or cartilage defects the values were < 0.54. The kappa values describing the correlation between the grade of bone uptake and the grade of the different MR findings was < 0.57.


CONCLUSIONS
Good agreement was found between increased bone uptake and MR detected subchondral lesion. The agreement between increased bone uptake and osteophytes or cartilage defects was in general poor as well as the agreement between the grade of bone uptake and the grade of the MR findings.
Quasi-one-dimensional metal oxide materials — Synthesis , properties and applications

Recent advances in the field of nanotechnology have led to the synthesis and characterization of an assortment of quasi-one-dimensional (Q1D) structures, such as nanowires, nanoneedles, nanobelts and nanotubes. These fascinating materials exhibit novel physical properties owing to their unique geometry with high aspect ratio. They are the potential building blocks for a wide range of nanoscale electronics, optoelectronics, magnetoelectronics, and sensing devices. Many techniques have been developed to grow these nanostructures with various compositions. Parallel to the success with group IV and groups III–V compounds semiconductor nanostructures, semiconducting metal oxide materials with typically wide band gaps are attracting increasing attention. This article provides a comprehensive review of the state-of-the-art research activities that focus on the Q1D metal oxide systems and their physical property characterizations. It begins with the synthetic mechanisms and methods that have been exploited to form these structures. A range of remarkable characteristics are then presented, organized into sections covering a number of metal oxides, such as ZnO, In2O3, SnO2, Ga2O3, and TiO2, etc., describing their electrical, optical, magnetic, mechanical and chemical sensing properties. These studies constitute the basis for developing versatile applications based on metal oxide Q1D systems, and the current progress in device development will be highlighted. # 2006 Elsevier B.V. All rights reserved.
A Metaobject Protocol for C++

This paper presents a metaobject protocol (MOP) for C++. This MOP was designed to bring the power of meta-programming to C++ programmers. It avoids penalties on runtime performance by adopting a new meta-architecture in which the metaobjects control the compilation of programs instead of being active during program execution. This allows the MOP to be used to implement libraries of efficient, transparent language extensions.