Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Prescription and Reconstruction of Brain MR Spectroscopy Data for Rapid Integration into the Clinical Workflow

Objectives: To implement and evaluate a fast, automated, end-to-end brain MR Spectroscopy workflow for rapid integration of metabolic parameters into clinical care. Materials and methods: An automated and reproducible atlas-based prescription for single and multi-voxel MR spectroscopy (MRS) data has been developed and combined with an online reconstruction that enables DICOM MRS results to be generated and sent to clinical PACS in realtime by the end of the MRI exam with the rest of the imaging data. The prescription method has been generalized for arbitrary classes of neurological exams through a library of templates that provide localization to specific anatomical locations. This enables rapid and consistent localization from serial follow-up studies, which is important for streamlining longitudinal comparisons. Results: When implemented in conjunction with spectroscopy sequences that are able to provide echo planar spatial encoding, the scan preparation time is reduced to approximately 1 minute, with a typical scan time of as little as 6 minutes for volumetric MRSI. Integration with automated online reconstruction methods that are able to utilize parallel computing strategies for analyzing large datasets permits delivery of the results in DICOM format to clinical PACS in real-time, and is critical for incorporating them into the radiological workflow. Total active console time for such studies including prescription, shimming, acquisition and report generation is 9.5 minutes. These methods have been implemented at UCSF, with 139 volumetric MRSI exams having been obtained from patients with brain tumors in the past year 18 months. 16 subjects scanned serially with the same prescription template had an average Dice overlap ratio of prescribed MRSI volumes of 0.979 ± 0.016. Conclusions: Robust, fast and automated MRS workflows, capable of delivering results to the reading room are feasible in clinically acceptable time frames. These workflows facilitate the integration of metabolic parameters into patient care. Neurological Disorders & Epilepsy Journal Automated Prescription and Reconstruction of Brain MR Spectroscopy Data for Rapid Integration into the Clinical Workflow. Neurol Disord Epilepsy J. 2017; 1(1):11
Taxi Driving Behavior Analysis in Latent Vehicle-to-Vehicle Networks: A Social Influence Perspective

With recent advances in mobile and sensor technologies, a large amount of efforts have been made on developing intelligent applications for taxi drivers, which provide beneficial guide and opportunity to improve the profit and work efficiency. However, limited scopes focus on the latent social interaction within cab drivers, and corresponding social propagation scheme to share driving behaviors has been largely ignored. To that end, in this paper, we propose a comprehensive study to reveal how the social propagation affects for better prediction of cab drivers' future behaviors. To be specific, we first investigate the correlation between drivers' skills and their mutual interactions in the latent vehicle-to-vehicle network, which intuitively indicates the effects of social influences. Along this line, by leveraging the classic social influence theory, we develop a two-stage framework for quantitatively revealing the latent driving pattern propagation within taxi drivers. Comprehensive experiments on a real-word data set collected from the New York City clearly validate the effectiveness of our proposed framework on predicting future taxi driving behaviors, which also support the hypothesis that social factors indeed improve the predictability of driving behaviors.
Kurdish Interdialect Machine Translation

This research suggests a method for machine translation among two Kurdish dialects. We chose the two widely spoken dialects, Kurmanji and Sorani, which are considered to be mutually unintelligible. Also, despite being spoken by about 30 million people in different countries, Kurdish is among less-resourced languages. The research used bi-dialectal dictionaries and showed that the lack of parallel corpora is not a major obstacle in machine translation between the two dialects. The experiments showed that the machine translated texts are comprehensible to those who do not speak the dialect. The research is the first attempt for inter-dialect machine translation in Kurdish and particularly could help in making online texts in one dialect comprehensible to those who only speak the target dialect. The results showed that the translated texts are in 71% and 79% cases rated as understandable for Kurmanji and Sorani respectively. They are rated as slightly-understandable in 29% cases for Kurmanji and 21% for Sorani.
Intrarenal angiotensin II plays an important role in renal fibrosis in primary IgA nephropathy.

Objective: To investigate the relationship of intrarenal angiotensin II (Ang II) expression with clinicpathological injury index and intrarenal expression and regulation of RAS (renin-angiotensin system) components in IgAN (immunoglobulin A nephropathy) patients. Material and methods: The expression of intrarenal renin, angiotensinogen (AGT), Ang II, Ang IIreceptor was examined by immunohistochemistry staining (IHCS). Clinic-pathological injury index included blood pressure, estimated glomerular filtration rate (eGFR), proteinuria and Katafuchi score. Results: Positive IHCS area of intrarenal Ang II was 32.73 ± 14.74%. There was a negative correlation between intrarenal Ang II and eGFR (r=-0.61, P<0.01), index of glomerular hypercellularity (ρ=-0.35, P<0.05). Intrarenal Ang II correlated positively with pathological chronicity index (ρ=0.39, P<0.05), index of interstitial cell infiltration (ρ=0.52, P<0.01), index of tubular atrophy (ρ=0.51, P<0.01), index of vessel wall thickening (ρ=0.36, P<0.05) and index of arteriolar hyalinosis (ρ=0.36, P<0.05). Intrarenal Ang II positively correlated with intrarenal renin and AGT (r=0.43, P<0.01 and r=0.3, P<0.05, respectively). No other correlation was evidenced between intrarenal expression of explored RAS components. Conclusions: Intrarenal Ang II plays an important role in renal fibrosis in IgAN, particularly at the tubulointerstitial level. Moreover, there is a tight regulation of the intrarenal RAS components in IgAN.
Wavelet-based Estimation of Hemodynamic Response Function from Fmri Data

We present a new algorithm to estimate hemodynamic response function (HRF) and drift components of fMRI data in wavelet domain. The HRF is modeled by both parametric and nonparametric models. The functional Magnetic resonance Image (fMRI) noise is modeled as a fractional brownian motion (fBm). The HRF parameters are estimated in wavelet domain by exploiting the property that wavelet transforms with a sufficient number of vanishing moments decorrelates a fBm process. Using this property, the noise covariance matrix in wavelet domain can be assumed to be diagonal whose entries are estimated using the sample variance estimator at each scale. We study the influence of the sampling rate of fMRI time series and shape assumption of HRF on the estimation performance. Results are presented by adding synthetic HRFs on simulated and null fMRI data. We also compare these methods with an existing method,(1) where correlated fMRI noise is modeled by a second order polynomial functions.
Exploring Valid Reference Genes for Quantitative Real-time PCR Analysis in Plutella xylostella (Lepidoptera: Plutellidae)

Abstract: Quantitative real-time PCR (qRT-PCR), a primary tool in gene expression analysis, requires an appropriate normalization strategy to control for variation among samples. The best option is to compare the mRNA level of a target gene with that of reference gene(s) whose expression level is stable across various experimental conditions. In this study, expression profiles of eight candidate reference genes from the diamondback moth, Plutella xylostella, were evaluated under diverse experimental conditions. RefFinder, a web-based analysis tool, integrates four major computational programs including geNorm, Normfinder, BestKeeper, and the comparative ΔCt method to comprehensively rank the tested candidate genes. Elongation factor 1 (EF1) was the most suited reference gene for the biotic factors (development stage, tissue, and strain). In contrast, although appropriate reference gene(s) do exist for several abiotic factors (temperature, photoperiod, insecticide, and mechanical injury), we were not able to identify a single universal reference gene. Nevertheless, a suite of candidate reference genes were specifically recommended for selected experimental conditions. Our finding is the first step toward establishing a standardized qRT-PCR analysis of this agriculturally important insect pest.
Principled Hidden Tagset Design for Tiered Tagging of Hungarian

For highly inflectional languages, the number of morpho-syntactic descriptions (MSD), required to descriptionally cover the content of a word-form lexicon, tends to rise quite rapidly, approaching a thousand or even more set of distinct codes. For the purpose of automatic disambiguation of arbitrary written texts, using such large tagsets would raise very many problems, starting from implementation issues of a tagger to work with such a large tagsets to the more theory-based difficulty of sparseness of training data. Tiered tagging is one way to alleviate this problem by reformulating it in the following way: starting from a large set of MSDs, design a reduced tagset, Ctag-set, manageable for the current tagging technology. We describe the details of the reduced tagset design for Hungarian, where the MSD-set cardinality is several thousand. This means that designing a manageable C-tagset calls for severe reduction in the number of the MSD features, a process that requires careful evaluation of the features.
A Simulation Study on Channel Estimation for Cooperative Communication System in Sand-dust Storm Environment

There are many factors that influence the propagation of electromagnetic wave in the sand-dust storm environment, the scattering effect of dust particle is one of the major factors, so this paper focuses on the dust particles scattering function. The scattering of dust particles inevitably brings the multipath transmission of the signal, multipath propagation will bring the multipath fading of the signal. In this paper, we first investigate the use of AF and DF modes in a sand-dust storm environment. Secondly, we present a low-order modulation method should be used in cooperative communication system. Lastly, we evaluate the system performance for both of the moving nodes and power allocation. Experimental results validate the conclusion of theoretical derivation: the multipath fading is one of the main factors that affect the quality of signal transmission. Cooperative communication technology has good anti-fading ability, which can guarantee the signal transmission timely and correctly.
Crystal structure of the NK 1 fragment of human hepatocyte growth factor at 2 . 0 Å resolution

Background: Hepatocyte growth factor (HGF) is a mitogen for hepatocytes and has also been implicated as an epithelial morphogen in tumor invasion. HGF activates its specific cellular receptor, c-met, through an aggregation mechanism potentiated by heparan sulfate glycosaminoglycans. HGF consists of an N-terminal (N) domain, four kringle domains (the first of which carries receptor-binding determinants), and an inactive serine-protease-like domain. NK1, a naturally occurring fragment of HGF, acts as an antagonist of HGF in the absence of heparin.
Sevoflurane preconditioning ameliorates traumatic spinal cord injury through caveolin-3-dependent cyclooxygenase-2 inhibition

Acute traumatic spinal cord injury (tSCI) results in a lifetime of paralysis associated with a host of medical complications. The developing secondary complications of tSCI may result in further chronic neurodegenerative diseases. Sevoflurane preconditioning (SF-PreCon) has shown guaranteed protective effects in myocardial or cerebral ischemic/reperfusion injury. However, the role of SF-PreCon in tSCI still remains to be elucidated. Here, we found that SF-PreCon ameliorated the developing secondary complications through reducing the apoptosis rate and the secretion of inflammatory cytokines in injured spinal cord tissues, and therefore enhancing the recovery after tSCI. Notably, we demonstrated that SF-PreCon ameliorates tSCI through inhibiting Cycloxygenase-2 (COX-2). Importantly, we verified that SF-PreCon inhibits the expression of COX-2 and reduces the apoptosis rate after tSCI via the induction of Caveolin-3 (Cav-3). Taken together, our results suggest that SF-PreCon ameliorates tSCI via Cav-3-dependent COX-2 inhibition and provide an economical and practical method against the secondary injury after tSCI.
Nanostructured Manganese Oxide Supported on Carbon Nanotubes for Electrocatalytic Water Splitting

Incipient wetness impregnation and a novel deposition symproportionation precipitation were used for the preparation of MnOx/CNT electrocatalysts for efficient water splitting. Nanostructured manganese oxides have been dispersed on commercial carbon nanotubes as a result of both preparation methods. A strong influence of the preparation history on the electrocatalytic performance was observed. The as‐prepared state of a 6.5 wt. % MnOx/CNT sample could be comprehensively characterized by comparison to an unsupported MnOx reference sample. Various characterization techniques revealed distinct differences in the oxidation state of the Mn centers in the as‐prepared samples as a result of the two different preparation methods. As expected, the oxidation state is higher and near +4 for the symproportionated MnOx compared to the impregnated sample, where +2 was found. In both cases an easy adjustability of the oxidation state of Mn by post‐treatment of the catalysts was observed as a function of oxygen partial pressure and temperature. Similar adjustments of the oxidation state are also expected to happen under water splitting conditions. In particular, the 5 wt. % MnO/CNT sample obtained by conventional impregnation was identified as a promising catalytic anode material for water electrolysis at neutral pH showing high activity and stability. Importantly, this catalytic material is comparable to state‐of‐art MnOx catalyst operating in strongly alkaline solutions and, therefore, offers advantages for hydrogen production from waste and sea water under neutral, hence, environmentally benign conditions.
Estimation of phase constrained MIMO transfer functions with application to flexible structures with

Abstract A computational scheme is proposed to estimate a state-space representation of MIMO transfer functions from frequency response measurements. The approach can constrain the phase curve of selected elements of the transfer function matrix to certain regions. Poles of the system are determined using a frequency domain subspace approach. The phase constraint is enforced by an LMI formulation based on the positive real lemma when the zeros of the system are estimated. The successful application of the algorithm to measurements from a cantilever beam with three collocated piezoelectric actuator/sensor pairs is demonstrated.
An analysis of a recreational hunter’s red deer tallies in the Tararua Ranges, North Island, New Zealand

We examined the jaw size, age and sex distribution of 324 red deer constituting a comprehensive record of all recreational hunting kills made by a single hunter of the Tararua ranges of North Island New Zealand over a period 20 years (1976-1996). The proportion of stags shot at times other than the rut (March April) was not significantly different to that in a sample of deer obtained by commercial helicopter hunting and did not change significantly after the first three years of hunting regardless of any effect of helicopter hunting. Conversely, significantly greater numbers of males were shot during the months of the rut and this proportion increased significantly after the first three years of hunting presumably as a result of increased selectivity and or skill. The recreational hunter harvested significantly greater numbers of older animals than did helicopter hunters. The proportion of older animals shot during, and at times other than the rut, increased significantly after the first three years of hunting. Analysis of jaw length versus age showed a significant increase in the jaw size of age cohorts born after 1976 i. e. after an increase in culling effort and was indicative of a general decline in population density during the period of the study. __________________________________________________________________________________________________________________________________
Large-scale randomized-coordinate descent methods with non-separable linear constraints

We develop randomized (block) coordinate descent (CD) methods for linearly constrained convex optimization. Unlike most CD methods, we do not assume the constraints to be separable, but let them be coupled linearly. To our knowledge, ours is the first CD method that allows linear coupling constraints, without making the global iteration complexity have an exponential dependence on the number of constraints. We present algorithms and analysis for four key problem scenarios: (i) smooth; (ii) smooth + nonsmooth separable; (iii) asynchronous parallel; and (iv) stochastic. We illustrate empirical behavior of our algorithms by simulation experiments.
Not a Victim: Challenges of Providing Services to Sexually Exploited Youth

The number of youth that have been sexually exploited continues to rise. In order to better understand the barriers sexually exploited youth may encounter when trying to seek services, this study explores social workers’ perspectives on why these barriers exist. Qualitative interviews were used to gather the experience of social workers who have worked with sexually exploited youth. Six themes consistent with research emerged; these themes are: characteristics of the girls, victim status, lack of awareness, support services, systemic responses and Minnesota responses. These themes show the various reasons youth may not seek services. Implications for clinical practice and future research are discussed. Running head: CHALLENGES OF PROVIDING SERVICES 3
Association of Rho-associated protein kinase 1 with E-cadherin complexes is mediated by p120-catenin

We show that Rho-associated protein kinase 1 coimmunoprecipitates with p120 and colocalizes to adherens junctions. p120 links ROCK1 to E-cadherin, as ROCK1 associates with wild-type, but not p120-uncoupled, E-cadherin. These data suggest that p120 regulates Rho activity at the cadherin complex via interaction with up- and downstream effectors, including ROCK1.
AMP-Activated Protein Kinase-Regulated Activation of the PGC-1α Promoter in Skeletal Muscle Cells

PGC‐1α is an important regulator of mitochondrial biogenesis in skeletal muscle. However, the transcriptional mechanisms controlling PGC‐1α expression in muscle remain to be clearly defined. We have isolated the proximal 2kb sequence of the PGC‐1α promoter from human genomic DNA. Analysis reveals that it contains putative binding sites for Sp1, ATF2/CREB, FKHR, GATA, SRF, MEF2, p53 and NF‐κB as well as multiple E Boxes. Using truncated deletions of the PGC‐1α promoter, we investigated the effect of AMPK activation by AICAR, a known mitochondrial biogenesis‐stimulating agent. AICAR treatment (1mM, 24hrs) increased promoter activity within the 848bp fragment of the PGC‐1α promoter activity by 3.4‐fold (p<0.001) in C2C12 muscle cells. This occurred concomitantly with 1.8‐ (p<0.05) and 2.2‐fold (p<0.05) increases in GATA‐EBox DNA‐binding and PGC‐1α mRNA expression, respectively. The AICAR effect, which is mediated via overlapping GATA/EBox binding sites, requires the cooperative actions of GATA‐4 and USF‐1. GATA‐4 overexpression increased PGC‐1α promoter activity 3.2‐fold (p<0.05), and was further enhanced by 1.4‐fold in the presence of AICAR. Our data define a novel pathway by which AMPK activation regulates PGC‐1α promoter activity via GATA‐4 and USF‐1, ultimately resulting in the induction of PGC‐1α mRNA expression. They also suggest that the modulation of the AMPK signaling pathway via GATA‐4 and/or USF‐1 could represent a potential therapeutic target to control PGC‐1α expression in skeletal muscle.
Scaling Laws for Large Ad-Hoc Wireless Networks with Wishart-Poisson Fading

In the analysis of large random wireless ad hoc networks, the underlying node distribution is almost ubiquitously assumed to be the homogeneous Poisson point process. Despite the nice analytical properties of such model, the spatial randomness has been, however, mainly exploited for connectivity and interference analysis, but has not yet been taken into account explicitly in the scaling laws evaluation. We move here a first step toward the evaluation of an upper bound on the aggregate throughput when the additional randomness due to the spatial node distribution is taken into account, together with the presence of power attenuation and random phase changes. This could be seen as a first attempt to connect some overoptimistic results based on stochastic channel model to more realistic analysis, relying on electromagnetic propagation arguments.
Simple and Adaptive Identification of Superspreaders by Flow Sampling

Abusive traffic caused by worms is increasing severely in the Internet. In many cases, worm-infected hosts generate a huge number of flows of small size during a short time. To suppress the abusive traffic and prevent worms from spreading, identifying these "superspreaders" as soon as possible and coping with them, e.g, disconnecting them from the network, is important. This paper proposes a simple and adaptive method of identifying superspreaders by flow sampling. By satisfying the given memory size and the requirement for the processing time, the proposed method can adaptively optimize parameters according to changes in traffic patterns.
Projective Feature Learning for 3D Shapes with Multi‐View Depth Images

Feature learning for 3D shapes is challenging due to the lack of natural paramterization for 3D surface models. We adopt the multi‐view depth image representation and propose Multi‐View Deep Extreme Learning Machine (MVD‐ELM) to achieve fast and quality projective feature learning for 3D shapes. In contrast to existing multi‐view learning approaches, our method ensures the feature maps learned for different views are mutually dependent via shared weights and in each layer, their unprojections together form a valid 3D reconstruction of the input 3D shape through using normalized convolution kernels. These lead to a more accurate 3D feature learning as shown by the encouraging results in several applications. Moreover, the 3D reconstruction property enables clear visualization of the learned features, which further demonstrates the meaningfulness of our feature learning.
The exon–intron gene structure upstream of the initiation codon predicts translation efficiency

Abstract Introns in mRNA leaders are common in complex eukaryotes, but often overlooked. These introns are spliced out before translation, leaving exon-exon junctions in the mRNA leaders (leader EEJs). Our multi-omic approach shows that the number of leader EEJs inversely correlates with the main protein translation, as does the number of upstream open reading frames (uORFs). Across the five species studied, the lowest levels of translation were observed for mRNAs with both leader EEJs and uORFs (29%). This class of mRNAs also have ribosome footprints on uORFs, with strong triplet periodicity indicating uORF translation. Furthermore, the positions of both leader EEJ and uORF are conserved between human and mouse. Thus, the uORF, in combination with leader EEJ predicts lower expression for nearly one-third of eukaryotic proteins.