Miracle-dz/UniFAR-FTUs huggingface dataset:
An Improved Instance Based K-Nearest Neighbor (IIBK) Classification of Imbalanced Datasets with Enhanced Preprocessing

The presence of data with skewed class distributions is a problem common to a variety of fields, including Bioinformatics, Computer science, Text classification, Remote-sensing, and Manufacturing industries. In Bioinformatics applications, the numbers of non-interacting proteins (majority class) are greater than number of interacting proteins (minority class) in predicting the protein-protein interactions. These results to imbalance dataset problem. Standard classification learning algorithms are often biased towards the majority class and therefore there is a higher misclassification rate for the minority class instances. In this work we focused on the minority class, for solving the imbalanced dataset problem. This research work consists of two stagespreprocessing and classification of imbalanced datasets. The imbalanced datasets were preprocessed using the SMOTE technique and it has been improved to show better results. Then the resultant dataset is classified using the existing J48 decision tree, Instance Based K-nearest neighbor (IBK), Support Vector Machine (SVM) and the proposed (IIBK) algorithm. Four datasets have been used for evaluation of the proposed algorithms and our results outperformed the other methods under the statistical comparative analysis.
Meta‐analysis of time‐to‐event data: a comparison of two‐stage methods

Meta‐analysis is widely used to synthesise results from randomised trials. When the relevant trials collected time‐to‐event data, individual participant data are commonly sought from all trials. Meta‐analyses of time‐to‐event data are typically performed using variants of the log‐rank test, but modern statistical software allows for the use of maximum likelihood methods such as Cox proportional hazards models or interval‐censored logistic regression. In this paper, the different approaches to the analysis of time‐to‐event data are examined and compared with show that log‐rank test approaches are in fact first‐order approximations to the maximum likelihood methods and that some methods assume proportional hazards, whereas others assume proportional odds. A simulation study is performed to compare the different methods, which shows that log‐rank test approaches give biased estimates when the underlying hazard ratio or odds ratio is far from unity. It also shows that proportional hazards methods give biased results when hazards are not proportional, and proportional odds methods give biased results when odds are not proportional. Maximum likelihood models should, therefore, be preferred to log‐rank test based methods for the meta‐analysis of time‐to‐event data and any such meta‐analysis should investigate whether proportional hazards or proportional odds assumptions are valid. Copyright © 2011 John Wiley & Sons, Ltd.
Developing a quantitative measure of alcohol consumption for genomic studies on prospective cohorts.

OBJECTIVE The purpose of this study was to develop a quantitative measure of alcohol consumption for gene-mapping studies. METHOD Using a sample of 3,787 young-adult twin women and an independent sample of 489 men and women from a college drinking study, we developed an alcohol-consumption factor score indexed by (1) maximum typical consumption (log-transformed quantity frequency [LQNTFRQ]), (2) maximum drinks in a 24-hours period (LMAXALC), (3) frequency of drinking five or more drinks per day (FIVE), and (4) frequency of drinking to intoxication (INTOX). We tested (1) for factorial and psychometric equivalence across samples and genders; (2) for construct validity and its equivalence, across samples and genders, using measures of tobacco and cannabis use and family history of alcoholism; and (3) to determine the heritability of the alcohol-consumption factor score using a genetic psychometric model. RESULTS A single-factor model fit well with factor loadings ranging from . 60 to . 90. With rare exception, we found support for measurement invariance across the two samples and across genders. Measures of nicotine and cannabis use as well as family history of alcoholism were associated, to a similar extent across samples and genders, with the underlying alcohol-consumption factor. Psychometric twin modeling revealed that each of the alcohol-consumption measures (h2=34%-47%) and the underlying factor score (h2=50%) were heritable, with the remainder of the variance attributable to individual-specific environmental factors. This moderately heritable alcohol-consumption factor also accounted for a majority of the genetic variance in LQNTFRQ, LMAXALC, FIVE, and INTOX. CONCLUSIONS Quantitative measures of alcohol consumption with the favorable attributes of measurement invariance, construct validity, and moderate heritability can greatly enhance future gene-mapping efforts, supplementing information afforded by conventional diagnostic measures of alcohol abuse/dependence.
Design of an orthotic device for full or partial gravity-balancing of a human upper arm during motion

Gravity balancing is often used in industrial machines to decrease the required actuator efforts during motion. In the literature, a number of methods have been proposed for gravity balancing that include counterweights, springs, and auxiliary parallelograms that determine the center of mass. However, these concepts have not yet been seriously applied to rehabilitation machines. This paper presents the underlying theory and design of an orthosis for the human upper arm that can fully or partially balance the human arm over the range of its motion. This design combines the use of auxiliary parallelograms to determine the center of mass along with springs to achieve a full or partial gravity balanced orthosis design. A first prototype is being constructed to demonstrate the effectiveness of the idea. Future prototypes will have parameters that will be tuned to the geometry and inertia of a human subject and tailor it to an individual's needs.
Molecular players in neutrophil chemotaxis—focus on PI3K and small GTPases

Neutrophil chemotaxis is a process by which individual cells sense a gradient of chemoattractant, polarize, and then migrate toward the chemoattractant. Many features of chemotaxis are shared with other forms of cell migration. We continue to expand our understanding of the mechanisms governing these features. The rapid process through which neutrophils polarize when placed into a gradient of chemoattractant remains least well‐understood. Several key molecular players involved in the regulation of polarization have been identified. However, crosstalk among the different molecular players is required to polarize the cell and to maintain cell polarity during directional migration. The mechanism(s) by which this occurs are the subject of current investigations using experimental and computational approaches. Here, we review progress in the field, putting recent observations into context with established findings. We concentrate on the signaling processes regulated by PI3Ks, their lipid products, the role of Rho‐family small GTPases, and crosstalk between these important families of regulators.
Vertical external-cavity surface-emitting laser for dual-wavelength generation

We report an optically pumped vertical external-cavity surface-emitting laser that is designed for emission at two wavelengths simultaneously. Single transverse mode continuous-wave (CW) operation is demonstrated at the wavelengths of 984 and 1042 nm. The device produces a CW optical power of 140 mW for the 984-nm component and 115 mW for the 1042-nm component, exhibiting over 10% efficiency. At a high pump power, self-pulsation of the components appeared on top of the CW-mode components. The maximum total output of 1 W was obtained at the pump power of 9 W.
Liver Iron Content Determined by MRI: Spin-Echo vs. Gradient-Echo

Abstract Purpose: Liver iron content (LIC) measurement plays a central role in the management of patients with transfusional iron overload. Calculating the LIC with data obtained from standardized MRI sequences represents an attractive alternative diagnostic possibility. The purpose of this study was to compare the LIC measurement obtained with gradient-echo (GRE) sequences to the mean liver proton transverse relaxation (R2) acquired with SE sequences. Materials and Methods: 68 patients with iron overload (median age: 24, range: 3 – 88) underwent 1.5 T MRI for liver iron content measurement. All patients received spin-echo (SE) and gradient-echo (GRE) sequences. Results: The two MRI methods revealed different liver iron content results although a significant correlation was found (r = 0.85, p < 0.001). Values evaluated using GRE sequences (median: 260 µmol/g dry weight [d. w.], range: 6 – 732) were generally higher than those obtained by SE examinations (median: 161 µmol /g d. w., range: 5 – 830). Conclusion: In conclusion, our study revealed different results for both MRI measurements, which could lead to different decisions concerning the management of chelation therapy in individual patients.
Voxel-based statistical analysis of cerebral glucose metabolism in patients with permanent vegetative state after acquired brain injury.

BACKGROUND Permanent vegetative state is defined as the impaired level of consciousness longer than 12 months after traumatic causes and 3 months after non-traumatic causes of brain injury. Although many studies assessed the cerebral metabolism in patients with acute and persistent vegetative state after brain injury, few studies investigated the cerebral metabolism in patients with permanent vegetative state. In this study, we performed the voxel-based analysis of cerebral glucose metabolism and investigated the relationship between regional cerebral glucose metabolism and the severity of impaired consciousness in patients with permanent vegetative state after acquired brain injury. METHODS We compared the regional cerebral glucose metabolism as demonstrated by F-18 fluorodeoxyglucose positron emission tomography from 12 patients with permanent vegetative state after acquired brain injury with those from 12 control subjects. Additionally, covariance analysis was performed to identify regions where decreased changes in regional cerebral glucose metabolism significantly correlated with a decrease of level of consciousness measured by JFK-coma recovery scale. Statistical analysis was performed using statistical parametric mapping. RESULTS Compared with controls, patients with permanent vegetative state demonstrated decreased cerebral glucose metabolism in the left precuneus, both posterior cingulate cortices, the left superior parietal lobule (P(corrected) < 0.001), and increased cerebral glucose metabolism in the both cerebellum and the right supramarginal cortices (P(corrected) < 0.001). In the covariance analysis, a decrease in the level of consciousness was significantly correlated with decreased cerebral glucose metabolism in the both posterior cingulate cortices (P(uncorrected) < 0.005). CONCLUSION Our findings suggest that the posteromedial parietal cortex, which are part of neural network for consciousness, may be relevant structure for pathophysiological mechanism in patients with permanent vegetative state after acquired brain injury.
F‐waves in neurogenic atrophy

F‐waves were determined in the peroneal nerves of 17 normal subjects, 11 amyotrophic lateral sclerosis (ALS) patients, and 13 patients with other disorders causing neurogenic atrophy (NA) in extensor digitorum brevis muscle. F‐waves were examined with regard to latency and waveform. Latency was increased above normal for both ALS and NA patients (P < 0.024 and P < 0.003, respectively). In normal subjects, the mean number of repeated responses (same latency and waveform) was 1.9 (r = 1.0–5.0), where 1.0 corresponds to no repeated response. In ALS patients, repeated responses were 2.9 (r = 1.2–7.8), which is not significantly different from normal (P < 0.099). In NA patients, repeated responses were 6.5 (r = 1.6–23), which is significantly above normal (P < 0.041). A dominant waveform occurred in 21.5% (mean) of responses in normal subjects (r = 4%–58%). In ALS and NA, corresponding values were 40.3% (r = 10%–88%) and 44.1% (r = 17%–100%), both of which were significantly above normal (P < 0.014 and P < 0.012, respectively). The distribution of F‐wave latencies is often nonrandom in normal, ALS, and NA subjects. The dominant F‐wave that was present in normal subjects and significantly increased in ALS and NA subjects may result from decreased numbers of motoneurons capable of contributing to the F‐response and would seem to be a useful additional measure of abnormality.
Long‐range connectivity of mouse primary somatosensory barrel cortex

The primary somatosensory barrel cortex processes tactile vibrissae information, allowing rodents to actively perceive spatial and textural features of their immediate surroundings. Each whisker on the snout is individually represented in the neocortex by an anatomically identifiable ‘barrel’ specified by the segregated termination zones of thalamocortical axons of the ventroposterior medial nucleus, which provide the primary sensory input to the neocortex. The sensory information is subsequently processed within local synaptically connected neocortical microcircuits, which have begun to be investigated in quantitative detail. In addition to these local synaptic microcircuits, the excitatory pyramidal neurons of the barrel cortex send and receive long‐range glutamatergic axonal projections to and from a wide variety of specific brain regions. Much less is known about these long‐range connections and their contribution to sensory processing. Here, we review current knowledge of the long‐range axonal input and output of the mouse primary somatosensory barrel cortex. Prominent reciprocal projections are found between primary somatosensory cortex and secondary somatosensory cortex, motor cortex, perirhinal cortex and thalamus. Primary somatosensory barrel cortex also projects strongly to striatum, thalamic reticular nucleus, zona incerta, anterior pretectal nucleus, superior colliculus, pons, red nucleus and spinal trigeminal brain stem nuclei. These long‐range connections of the barrel cortex with other specific cortical and subcortical brain regions are likely to play a crucial role in sensorimotor integration, sensory perception and associative learning.
Analysis of nonadditive protein accumulation in young primary roots of a maize (Zea mays L.) F1‐hybrid compared to its parental inbred lines

Heterosis describes the superior performance of heterozygous F1‐hybrids compared to their homozygous parental inbred lines. Heterosis is already manifested during early maize (Zea mays L.) primary root development. In this study, the most abundant soluble proteins have been investigated before the phenotypic manifestation of heterosis in 3.5‐day‐old primary roots in the flint inbred line UH002, the dent inbred line UH301 and the corresponding hybrid UH301×UH002. In CBB‐stained 2‐DE gels, 150 of 304 detected proteins (49%) were accumulated in a nonadditive fashion in the hybrid compared to the average of their parental inbred lines (Student's t‐test: p < 0.05). Remarkably, expression of 51% (76/150) of the nonadditively accumulated proteins exceeded the high parent or was below the low parent. ESI‐MS/MS identified 75 of the 76 proteins that belonged to these expression classes. The most abundant functional classes among the 75 proteins that were encoded by 60 different genes were metabolism (58%) and disease and defense (19%). Nonadditive protein accumulation in primary roots of maize hybrids might be associated with heterosis manifestation. Identification of these proteins could therefore contribute to the better understanding of the molecular basis of heterosis.
Evaluation of commercial vancomycin agar screen plates for detection of vancomycin-resistant enterococci

Brain heart infusion-6-micrograms/ml vancomycin agar plates obtained from five commercial sources (B-D Microbiology Systems, Carr-Scarborough Microbiologicals, MicroBio Products, PML Microbiologicals, and REMEL) were evaluated with 714 enterococci for detection of vancomycin resistance. All 465 (100%) vancomycin-resistant enterococci (MIC > or = 32 micrograms/ml) were detected by each manufacturer's agar screen plate, and each manufacturer's agar screen plate detected at least 99% of the 177 vancomycin-susceptible enterococci (MIC < or = 4 micrograms/ml). Detection of the 72 vancomycin-intermediate enterococci (MIC = 6 to 16 micrograms/ml) ranged from 94% for B-D Microbiology Systems to 99% for PML Microbiologicals.
Insulin Sensitivity and Acute Insulin Response in African-Americans, Non-Hispanic Whites, and Hispanics With NIDDM: The Insulin Resistance Atherosclerosis Study

NIDDM is usually characterized by β-cell failure decreased and insulin sensitivity. It has been reported that a high proportion of African-American NIDDM subjects are insulin sensitive. To examine this issue, we determined insulin sensitivity (SI) in 479 NIDDM subjects by minimal model analyses of frequently sampled intravenous glucose tolerance (FSIGT) from the Insulin Resistance Atherosclerosis Study (IRAS), a large multicenter study of insulin sensitivity and cardiovascular risk in African-Americans, Hispanics, and non-Hispanic whites. The African-Americans and non-Hispanic whites were sampled in Los Angeles and Oakland, California. The non-Hispanic whites and Hispanics were sampled in San Antonio, Texas, and San Luis Valley, Colorado. We defined the proportion of insulin-sensitive (SI) subjects as ≥1.61 min−1 · μU−1 · ml−1, which is above the median for nondiabetic subjects of all ethnic groups in the IRAS. Using this definition, the proportion of insulin-sensitive diabetic subjects was very low in all ethnic groups (non-Hispanic whites [14.3%] vs. African- Americans [6.5%], P = 0.039 in Los Angeles and Oakland; non-Hispanic whites [6.8%] vs. Hispanics [4.9%], P = 0.737 in San Luis Valley and San Antonio). These results were also similar in newly diagnosed mildly hyperglycemic diabetic subjects. In addition, these results were not affected by the adjustment for differences in obesity, body fat distribution, and severity of hyperglycemia. Even in nonobese subjects (with BMI <30 kg/m2), the proportion of insulin-sensitive subjects (S1 ≥1.61 min−1 · μU−1 · ml−1) was low (3.6–9.7%). The acute insulin response (AIR) was significantly higher in African-Americans than in non-Hispanic whites; there were no ethnic differences in AIR between Hispanics and non–Hispanic whites. There were no significant ethnic differences for non-insulin-mediated glucose disposal (SG). We conclude that the number of insulinsensitive NIDDM subjects is low and similar among non-Hispanic whites, Hispanics, and African-Americans in the U.S.
State-Regularized Policy Search for Linearized Dynamical Systems

Trajectory-Centric Reinforcement Learning and Trajectory Optimization methods optimize a sequence of feedback-controllers by taking advantage of local approximations of model dynamics and cost functions. Stability of the policy update is a major issue for these methods, rendering them hard to apply for highly nonlinear systems. Recent approaches combine classical Stochastic Optimal Control methods with information-theoretic bounds to control the step-size of the policy update and could even be used to train nonlinear deep control policies. These methods bound the relative entropy between the new and the old policy to ensure a stable policy update. However, despite the bound in policy space, the state distributions of two consecutive policies can still differ significantly, rendering the used local approximate models invalid. To alleviate this issue we propose enforcing a relative entropy constraint not only on the policy update, but also on the update of the state distribution, around which the dynamics and cost are being approximated. We present a derivation of the closed-form policy update and show that our approach outperforms related methods on two nonlinear and highly dynamic simulated systems.
The formation of neuromuscular synapses.

The formation of synapses requires a series of steps including the generation of neurons and their target cells, the guidance of axons to their targets, and the induction of a specialized presynaptic terminal and postsynaptic membrane. This review is primarily concerned with the inductive events that lead to postsynaptic differentiation. Because this phase of synapse formation begins only after motor neurons have navigated to their target muscle cells, the first section of this review summarizes our current understanding of the principles that govern the guidance of motor axons to skeletal muscle cells. The second section will review our current knowledge of signaling molecules and mechanisms that are critical for inducing postsynaptic differentiation. Although the principles and mechanisms of synapse formation are likely to be similar in the PNS and the CNS, much of our understanding about the mechanisms of synapse formation arises from studies of the vertebrate neuromuscular synapse.
A modified expectation maximization algorithm for penalized likelihood estimation in emission tomography

The maximum likelihood (ML) expectation maximization (EM) approach in emission tomography has been very popular in medical imaging for several years. In spite of this, no satisfactory convergent modifications have been proposed for the regularized approach. Here, a modification of the EM algorithm is presented. The new method is a natural extension of the EM for maximizing likelihood with concave priors. Convergence proofs are given.
A rabbit model demonstrates the influence of cartilage thickness on intra‐articular drug delivery and retention within cartilage

For evaluation of new approaches to drug delivery into cartilage, the choice of an animal model is critically important. Since cartilage thickness varies with animal size, different levels of drug uptake, transport and retention should be expected. Simple intra‐articular injection can require very high drug doses to achieve a concentration gradient high enough for drug diffusion into cartilage. New approaches involve nanoparticle delivery of functionalized drugs directly into cartilage; however, diffusion‐binding kinetics proceeds as the square of cartilage thickness. In this study, we demonstrate the necessity of using larger animals for sustained intra‐cartilage delivery and retention, exemplified by intra‐articular injection of Avidin (drug‐carrier) into rabbits and compared to rats in vivo. Penetration and retention of Avidin within cartilage is greatly enhanced by electrostatic interactions. Medial tibial cartilage was the thickest of rabbit cartilages, which generated the longest intra‐cartilage half‐life of Avidin (τ1/2 = 154 h). In contrast, Avidin half‐life in thinner rat cartilage was 5–6 times shorter (τ1/2 ∼ 29 h). While a weak correlation (R2 = 0.43) was found between Avidin half‐lives and rabbit tissue GAG concentrations, this correlation improved dramatically (R2 = 0.96) when normalized to the square of cartilage thickness, consistent with the importance of cartilage thickness to evaluation of drug delivery and retention. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:660–667, 2015.