LLukas22/scidocs huggingface dataset:
Classification Techniques in Gene Expression Microarray Data

Cancer nowadays is a common and heterogeneous disease affecting all people of all ages. Gene expression data can serve to understand cancer or other types of disease well. Building classification system using gene expression dataset that can properly classify new samples is a challenging task due to the nature of gene expression data that is usually composed of dozens of samples characterized by thousands of genes. This paper put a light on different classification methods used in classifying gene expression data including SVM, NB, C4.5 and some of the state-of-the-art techniques. Keywords— Gene expression microarray; data mining techniques; cancer classification; classification; microarray data analysis
Effects of a preoperative simplified home rehabilitation education program on length of stay of total knee arthroplasty patients.

UNLABELLED
In patients with severe knee osteoarthritis (OA), total knee arthroplasty (TKA) is performed for both symptom relief and to achieve better function in daily life. Implementation of efficient TKA rehabilitation programs with shorter length of stay (LOS) and reduced medical expenditures is an important issue in clinical practice. However, the effectiveness of preoperative rehabilitation programs is still under debate. Most preoperative rehabilitation programs last many weeks and may be more expensive than TKA. The purpose of this study was to investigate the effects of a simplified, easy-to-learn, and less time-consuming preoperative rehabilitation education program on TKA patients.


PATIENTS AND METHODS
In this randomized controlled study, we allocated all the patients into study and control group according to chart number. The study group, which comprised 126 patients, participated in a 40-min preoperative home rehabilitation education program 4 weeks prior to TKA. One hundred seventeen patients in the control group did not participate in this preoperative program.


RESULTS
The study group required a shorter hospital LOS (mean: 7.12 days; P=0.027) and had less hospitalization-related medical expenditures (mean: 123726 New Taiwan dollars [NTD], equivalent to 4266.4 United States dollars [USD] or 3022.1 [Euros]), (P=0.001) than the control group. However, the study group showed no significant improvement in function when compared to the control group.


DISCUSSION
Our study demonstrates that a simplified preoperative rehabilitation program can reduce LOS and increase cost savings. This program was recommended as a routine protocol for OA patients before admission for TKA.
IEEE Recommended Practice for Speech Quality Measurements

The IEEE Recommended Practice for Speech Quality Measurement is the product of roughly six years of study, discussion, writing, and rewriting by a diligent team of scientists representing a broad range of disciplines and research institutions. We will attempt to recognize here all those who participated, ranging from the dogged individuals who were with the committee for its entire life to those who participated in at least one meeting.
Multi-aspect opinion polling from textual reviews

This paper presents an unsupervised approach to aspect-based opinion polling from raw textual reviews without explicit ratings. The key contribution of this paper is three-fold. First, a multi-aspect bootstrapping algorithm is proposed to learn from unlabeled data aspect-related terms of each aspect to be used for aspect identification. Second, an unsupervised segmentation model is proposed to address the challenge of identifying multiple single-aspect units in a multi-aspect sentence. Finally, an aspect-based opinion polling algorithm is presented. Experiments on real Chinese restaurant reviews show that our opinion polling method can achieve 75.5% precision performance.
Stabilization of trajectories for systems with nonholonomic constraints

A new technique for stabilizing nonholonomic systems to trajectories is presented. It is well known (see [2]) that such systems cannot be stabilized to a point using smooth static-state feedback. In this note, we suggest the use of control laws for stabilizing a system about a trajectory, instead of a point. Given a nonlinear system and a desired (nominal) feasible trajectory, the note gives an explicit control law which will locally exponentially stabilize the system to the desired trajectory. The theory is applied to several examples, including a car-like robot.
Occupational risk factors for Wegener's granulomatosis: a case-control study.

BACKGROUND
Wegener's granulomatosis is a systemic vasculitis of unknown aetiology. Previous studies have presented environmental exposures such as silica and farming as potential risk factors.


OBJECTIVE
To investigate the potential risk for Wegener's granulomatosis associated with occupations involving contact with animals and various airway exposures, using a population-based approach.


METHODS
In the Swedish Register of inpatient care 2288 cases with Wegener's granulomatosis were identified. Ten matched controls for every case were selected from the Swedish Population Register. By linking the cases and controls to the Swedish population censuses, information on employments before the diagnosis of Wegener's granulomatosis was collected. Relative risks were assessed as odds ratios using conditional logistic regression.


RESULTS
Odds ratios for specific occupations ranged from 0.6 to 1.9, and centred symmetrically around 1. No statistically significant increased risk was noted for the investigated occupations.
On the Planning of Science Island of Chinese Academy of Sciences

The paper introduces the planning of Science Island of China Academy of Science, spatial and functional distribution, ecological greensystem, and analyzes the basic planning methods of Science Island, and explores the application of ecological planning methods and integralplanning methods to the planning of Science Island.[
Blood pressure control in ultra-early basal ganglia intracerebral hemorrhage.

OBJECTIVE
We performed this study to investigate the effect of blood pressure control in ultra-early basal ganglia intracerebral hemorrhage.


PATIENTS AND METHODS
120 patients with ultra-early basal ganglia intracerebral hemorrhage were randomly divided into experimental group (strengthened antihypertensive) and control (normal antihypertensive). Each group consists of 60 patients, whose contractive pressure were controlled by intravenous antihypertensive drugs among 130-140 mmHg and 160-180 mmHg respectively for 24 h, after 1 h of beginning treatment. They were all evaluated by NIH Stroke Scale (NIHSS) before and after the treatment. Cranial CT, hematoma volume, hematoma enlargement, edema volume, serum matrix metalloproteinase-9 level were performed and compared between groups.


RESULTS
After 24 h, hematoma volume and hematoma enlargement in the experimental group was significantly lower than control (p < 0.05). After 14 days, NIHSS score in the experimental group was significantly lower than control (p < 0.05). Cerebral edema amount and serum MMP-9 level in the experimental group were significantly lower than control after 5 days and 14 days.


CONCLUSIONS
Ultra-early basal ganglia intracerebral hemorrhage can remarkably reduce hematoma enlargement, cerebral edema, serum MMP-9 level, and improve the neurological function.
Production of lactic acid from hemicellulose extracts by Bacillus coagulans MXL-9

Bacillus coagulans MXL-9 was found capable of growing on pre-pulping hemicellulose extracts, utilizing all of the principle monosugars found in woody biomass. This organism is a moderate thermophile isolated from compost for its pentose-utilizing capabilities. It was found to have high tolerance for inhibitors such as acetic acid and sodium, which are present in pre-pulping hemicellulose extracts. Fermentation of 20 g/l xylose in the presence of 30 g/l acetic acid required a longer lag phase but overall lactic acid yield was not diminished. Similarly, fermentation of xylose in the presence of 20 g/l sodium increased the lag time but did not affect overall product yield, though 30 g/l sodium proved completely inhibitory. Fermentation of hot water-extracted Siberian larch containing 45 g/l total monosaccharides, mainly galactose and arabinose, produced 33 g/l lactic acid in 60 h and completely consumed all sugars. Small amounts of co-products were formed, including acetic acid, formic acid, and ethanol. Hemicellulose extract formed during autohydrolysis of mixed hardwoods contained mainly xylose and was converted into lactic acid with a 94% yield. Green liquor-extracted hardwood hemicellulose containing 10 g/l acetic acid and 6 g/l sodium was also completely converted into lactic acid at a 72% yield. The Bacillus coagulans MXL-9 strain was found to be well suited to production of lactic acid from lignocellulosic biomass due to its compatibility with conditions favorable to industrial enzymes and its ability to withstand inhibitors while rapidly consuming all pentose and hexose sugars of interest at high product yields.
Effectiveness and neural mechanisms associated with tDCS delivered to premotor cortex in stroke rehabilitation: study protocol for a randomized controlled trial

BACKGROUND
More than 60% of stroke survivors experience residual deficits of the paretic upper limb/hand. Standard rehabilitation generates modest gains. Stimulation delivered to the surviving Primary Motor Cortex in the stroke-affected hemisphere has been considered a promising adjunct. However, recent trials challenge its advantage. We discuss our pilot clinical trial that aims to address factors implicated in divergent success of the approach. We assess safety, feasibility and efficacy of targeting an alternate locus during rehabilitation- the premotor cortex. In anticipating variance across patients, we measure neural markers differentiating response from non-response.


METHODS/DESIGN
In a randomized, sham-controlled, double-blinded pilot clinical study, patients with chronic stroke (n = 20) are assigned to receive transcranial direct current stimulation delivered to the premotor cortex or sham during rehabilitation of the paretic arm/hand. Patients receive the designated intervention for 30 min, twice a day for 3 days a week for 5 weeks. We assess hand function and patients' reports of use of paretic hand. A general linear mixed methods model will analyze changes from pre- to post-intervention. Responders and non-responders will be compared upon baseline level of function, and neural substrates, including function and integrity of output tracts, bi-hemispheric balance, and lesion profile. Incidence of adverse events will be compared using Fisher's Exact test, while rigor of blinding will be assessed with Chi-square analysis to ascertain feasibility.


DISCUSSION
Variable success of cortical stimulation in rehabilitation can be related to gaps in theoretical basis and clinical investigation. Given that most patients with severe deficits have damage to the primary motor cortex or its output pathways, it would be futile to target stimulation to this site. We suggest targeting premotor cortex because it contributes substantially to descending output, a role that is amplified with greater damage to the motor cortex. With regards to clinical investigation, paired cortical stimulation in rehabilitation has been compared to rehabilitation alone in unblinded trials or to unconvincing sham conditions. Transcranial direct current stimulation, a noninvasive technique of brain stimulation, which offers a more effective placebo and has a favorable safety-feasibility profile, may improve scientific rigor. Neural markers of response would help inform patient selection for future clinical trials so we can address limitations of recent negative studies.


TRIAL REGISTRATION
NCT01539096.
A comparison of dual vs. triple antiplatelet therapy in patients with non-ST-segment elevation acute coronary syndrome: results of the ELISA-2 trial.

AIMS
To compare dual vs. triple antiplatelet pre-treatment in patients with non-ST-elevation acute coronary syndrome (NSTE ACS) who were planned for early catheterization.


METHODS AND RESULTS
A total of 328 consecutive patients with NSTE ACS were included and were randomized to pre-treatment with dual (n = 166, aspirin, clopidogrel 600 mg) or triple antiplatelet therapy (n = 162, aspirin, clopidogrel 300 mg, and Tirofiban). The primary endpoint was enzymatic infarct size, defined as cumulative LDH release (LDHQ(48)). Initial TIMI flow of the culprit vessel was a pre-specified secondary endpoint. Angiography was performed in 98% of patients at a median of 23 h after admission. Enzymatic infarct size (median, 25-75%) was 166 (60-349) IU/L in the triple group compared with 193 (75-466) IU/L in the dual group (P = 0.2). Initial TIMI 3 flow of the culprit vessel was significantly more often observed after triple antiplatelet therapy (67 vs. 47%, P = 0.002). At 30 days follow-up, myocardial infarction (MI) occurred in 46% of patients in the triple antiplatelet group, compared with 57% in the dual antiplatelet group, P = 0.052. No significant difference in bleeding was present.


CONCLUSION
This study showed that in patients with NSTE ACS, triple antiplatelet pre-treatment was associated with a non-significant reduction in enzymatic infarct size, a significantly better initial perfusion of the culprit vessel, and a trend towards a better survival without death or MI. Further, large-scale studies should be performed to find whether the beneficial trend in favour of triple antiplatelet pre-treatment can be reproduced.
Omega-3 fatty acid treatment, with or without cytidine, fails to show therapeutic properties in bipolar disorder: a double-blind, randomized add-on clinical trial.

OBJECTIVE
This study aimed to test the effects of omega-3 fatty acids (O3FA), given as fish oil capsules, with and without oral cytidine (CYT), a pyrimidine with reported preclinical and clinical antidepressant-like effects, in patients with bipolar disorder (BD).


METHODS
A total of 45 outpatients with diagnosed BD (type I) according to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition - Text Revision, were recruited for this 4-month, randomized, double-blind, placebo-controlled, add-on study. Treatment groups were (1) oral CYT + O3FA, (2) placebo + O3FA, and (3) placebo + placebo control. O3FA was given 2 g twice a day and CYT was administered as 1 g twice a day.


RESULTS
There was no statistically significant difference among the groups in the primary outcome: study retention. Clinical measures improved in all treatment groups, and there were no significant differences between groups, including change in probability of symptoms of depression or mania, change in positive ratings of depression or mania, or change in Global Assessment of Functioning scores. Neither CYT + O3FA nor placebo + O3FA treatment was superior to placebo treatment. Rather, there was a statistically nonsignificant trend for both groups treated with O3FA to do worse than the placebo group.


CONCLUSIONS
Despite preclinical studies suggesting that the effect of O3FA might be augmented with pyrimidines, add-on CYT did not substantially improve mood symptoms in BD. In addition, although a power analysis indicated that the sample size would be adequate to see beneficial effects similar to those previously reported, O3FA treatment by itself was not superior to placebo for BD.
A Traceability Technique for Specifications

Traceability in software involves discovering links between different artifacts, and is useful for a myriad of tasks in the software life cycle. We compare several different Information Retrieval techniques for this task, across two datasets involving real-world software with the accompanying specifications and documentation. The techniques compared include dimensionality reduction methods, probabilistic and information theoretic approaches, and the standard vector space model.
Building Libraries in Prolog

While Prolog has proven useful for writing programs in a variety of domains, it suffers from its lack of support for modularity, particularly for building libraries of routines and data. This paper points out some problems with standard Prolog that make libraries inconvenient. It then describes a solution to those problems based on the concepts of modules and database views.
Earthquake Propensity and the Politics of Mortality Prevention

Governments can significantly reduce earthquake mor tality by enforcing quake-proof construction regulation. We examine why many govern me ts do not. First, mortality is lower in countries with higher earthquake propensity, whe re the payoffs to investments in mortality prevention are greater. Second, the opportunity cos ts of these investments are higher in poorer countries; mortality is correspondingly less respon sive to propensity in poor countries. Third, mortality is higher at any level of quake propensit y when governments have fewer incentives to provide public goods, such as in autocracies wit h less institutionalized ruling parties or in more corrupt countries.
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration

Wikidata is a world readable and writable knowledge base maintained by the Wikimedia Foundation. It offers the opportunity to collaboratively construct a fully open access knowledge graph spanning biology, medicine, and all other domains of knowledge. To meet this potential, social and technical challenges must be overcome most of which are familiar to the biocuration community. These include community ontology building, high precision information extraction, provenance, and license management. By working together with Wikidata now, we can help shape it into a trustworthy, unencumbered central node in the Semantic Web of biomedical data. Keywords—wikidata; semantic web; ontology; crowdsourcing; wiki; biocuration; knowledge graph;
Randomized Trial of Treat and Extend Ranibizumab with and without Navigated Laser for Diabetic Macular Edema: TREX-DME 1 Year Outcomes.

PURPOSE
To compare monthly dosing with a treat and extend algorithm using ranibizumab 0.3 mg with and without angiography-guided macular laser photocoagulation for center-involving diabetic macular edema (DME).


DESIGN
Multicenter, prospective, randomized clinical trial.


PARTICIPANTS
A total of 150 eyes from 116 subjects were randomized into 3 cohorts: Monthly (n = 30), TReat and EXtend without macular laser photocoagulation (TREX; n = 60), and treat and extend with angiography-GuIded macular LAser photocoagulation (GILA; n = 60).


METHODS
Monthly cohort eyes received ranibizumab 0.3 mg every 4 weeks. Eyes in the TREX and GILA cohorts received 4 monthly injections of ranibizumab 0.3 mg followed by a treat and extend algorithm based on disease activity. Eyes in the GILA cohort also received angiography-guided macular laser photocoagulation at month 1 and again every 3 months for microaneurysm leakage.


MAIN OUTCOME MEASURES
Change in mean best-corrected visual acuity (BCVA), mean central retinal thickness (CRT), number of injections from baseline to 1 year, and percentage gaining/losing 2 and 3 lines of vision.


RESULTS
Baseline demographics were well balanced among the cohorts. A total of 137 eyes (91%) completed the 1-year end point visit. At 1 year, the mean BCVA improved by 8.6, 9.6, and 9.5 letters in the Monthly, TREX, and GILA cohorts, respectively (P = 0.8). There was no significant difference between the cohorts in the percentage gaining/losing 2 and 3 lines of vision. The CRT improved by 123 μm, 146 μm, and 166 μm in the Monthly, TREX, and GILA cohorts, respectively (P = 0.47). The mean number of macular laser treatments in the GILA cohort at 1 year was 2.9 (range, 1-4). The number of injections was significantly reduced in both the TREX (10.7) and GILA (10.1) cohorts compared with the Monthly cohort (13.1, P < 0.001). There were no cases of endophthalmitis, and the total incidence of Anti-Platelet Trialists' Collaboration events was 4.7%.


CONCLUSIONS
This prospective, randomized trial found that treat and extend dosing of ranibizumab 0.3 mg with and without angiography-guided macular laser photocoagulation significantly decreased the number of injections given while providing similar visual and anatomic outcomes compared with monthly dosing at 1 year. Adding angiography-guided laser photocoagulation to this dosing algorithm did not significantly improve outcomes at 1 year.
Parallel improvement of cognitive functions and P300 latency following donepezil treatment in patients with Alzheimer's disease: a case-control study.

PURPOSE
To evaluate the effect of donepezil, one of the cholinesterase inhibitors, on P300 measurements in patients with Alzheimer's disease (AD) and investigate the relationship between the subfactors of cognitive performance and P300 components.


METHODS
One hundred outpatients with AD were evaluated for cognitive function (cognitive ability screening instrument) and event-related potentials before and after 22 to 23 weeks of treatment with donepezil (5 mg/day). Twenty age-matched normal control subjects were recruited.


RESULTS
The patients with AD showed prolonged P300 and N200 latency, no significant differences in N100 and P200 components, and poor performance in neuropsychological assessments compared with control subjects at baseline. After donepezil treatment, the patients with AD had reduction in P300 latency at Pz lead, which was associated with a parallel improvement in cognitive function in terms of remote memory, recent memory, visual instruction, and orientation. The pre-post treatment difference of P300 latency significantly correlated with the cognitive ability screening instrument score difference and recent memory score difference, respectively.


CONCLUSIONS
The patients with AD still had intact early sensory processing but impaired higher-level cognitive processes that could influence behavior deviation. The donepezil treatment, which enhances higher-level cognitive processing time, revealed that P300 latency decreases as cognitive capability increases, especially improved in recent memory.
Oxidation of mannosyl oligosaccharides by hydroxyl radicals as assessed by electrospray mass spectrometry.

The hydroxyl radicals are widely implicated in oxidation of carbohydrates during biological and industrial processes being responsible for their structural modifications and causing functional damage. The identification of intermediate oxidation products is hampered by a lack of reliable sensible methods for their detection. In this study, the oxidation of two models of galactomannans (Man(3) and GalMan(2)) has been studied in reaction with hydroxyl radical generated by Fenton reaction. The oxidation patterns were assessed using preparative ligand-exchange/size-exclusion chromatography (LEX/SEC) coupled with tandem electrospray mass spectrometry (ESI-MS/MS). This allowed the identification of derived oligosaccharides (OS) containing hexuronic, hexonic, pentonic and erythronic acid residues and neutral OS bearing hydroperoxy, hydrated carbonyl moieties and residues from pyranosyl ring cleavage. The depolymerization products have been also detected upon oxidation of oligomers. This study allowed developing a simple, effective 'fingerprinting' protocol for detecting the damage done to mannans by oxidative radicals.
Words or Characters? Fine-grained Gating for Reading Comprehension

Previous work combines word-level and character-level representations using concatenation or scalar weighting, which is suboptimal for high-level tasks like reading comprehension. We present a fine-grained gating mechanism to dynamically combine word-level and character-level representations based on properties of the words. We also extend the idea of fine-grained gating to modeling the interaction between questions and paragraphs for reading comprehension. Experiments show that our approach can improve the performance on reading comprehension tasks, achieving new state-of-the-art results on the Children’s Book Test and Who Did What datasets. To demonstrate the generality of our gating mechanism, we also show improved results on a social media tag prediction task.1