Miracle-dz/UniFAR-FTUs huggingface dataset:
Study on the dereverberation of speech based on temporal envelope filtering

The authors explore speech dereverberation techniques whose principle is the recovery of the envelope modulations of the original (anechoic) speech. Based on their previous experience with such kind of processing for additive noise reduction applications, they apply a data designed filter-bank technique to the reverberant speech. Comparing their results with other works they discuss the effectiveness and limitations of this type of approaches.
A computational framework for driver's visual attention using a fully convolutional architecture

It is a challenging and important task to perceive and interact with other traffic participants in a complex driving environment. The human vision system plays one of the crucial roles to achieve this task. Particularly, visual attention mechanisms allow a human driver to cleverly attend to the salient and relevant regions of the scene to further make necessary decisions for the safe driving. Thus, it is significant to investigate human vision systems with great potential to improve assistive, and even autonomous, vehicular technologies. In this paper, we investigate driver's gaze behavior to understand visual attention. We, first, present a Bayesian framework to model visual attention of a human driver. Further, based on the framework, we develop a fully convolutional neural network to estimate the salient region in a novel driving scene. We systematically evaluate the proposed method using on-road driving data and compare it with other state-of-the-art saliency estimation approaches. Our analyses show promising results.
Characterization of Enterovirus Isolates from Patients with Heart Muscle Disease in a Selenium-Deficient Area of China

ABSTRACT An association of enterovirus infection with endemic cardiomyopathy (Keshan disease [KD]) and outbreaks of myocarditis in selenium-deficient rural areas of southwestern China has been established. Enteroviruses have been isolated from patients with KD or during outbreaks of myocarditis in last two decades. Six of these isolates grew readily in cell lines (Vero or HEp-2) and were investigated by a novel molecular typing method apart from serotyping and pathogenicity. A neutralization assay identified two isolates from KD as coxsackievirus serotype B2 (CVB2) and two isolates from myocarditis as coxsackievirus serotype B6 (CVB6) but failed to type the remaining two isolates, also from myocarditis. Direct nucleotide sequencing of reverse transcription-PCR products amplified from the 5′ nontranslated region (5′NTR) of these viruses confirmed that they belong to a phylogenetic cluster consisting of coxsackie B-like viruses, including some echovirus serotypes. Sequence analysis of the coding region for viral capsid protein VP1 showed that two isolates serotyped as CVB2 have the highest amino acid sequence homology with CVB2 and that the remaining four isolates, two CVB6 and the two unknown serotypes, are most closely related to the sequence of CVB6. Sequences among these isolates varied from 82.3 to 99% in the 5′NTR and from 69 to 99% in VP1, indicating no cross contamination. The pathogenicity of these viruses in adult and suckling mice was assessed. None caused pathologic changes in the hearts of adult MF-1 or SWR mice, although pancreatitis was evident. However, the four CVB6-like viruses caused death in suckling mice, similar to a virulent coxsackievirus group B3 laboratory strain. In conclusion, the sequence data confirm that coxsackievirus group B serotypes are predominant in the region in which KD is endemic and may be the etiological agents in outbreaks of myocarditis. VP1 genotyping of enteroviruses is accurate and reliable. Animal experiments indicate that isolates may differ in pathogenicity.
L12-Strengthened Cobalt-Base Superalloys

The discovery of the γ′-Co3(Al,W) phase with an L12 structure provided Co-base alloys with a new strengthening mechanism, enabling a new class of high-temperature material: Co-base superalloys. This review discusses the current understanding of the phase stability, deformation, and oxidation behaviors of γ′ single-phase and γ + γ′ two-phase alloys in comparison with Ni-base γ′-L12 phase and γ + γ′ superalloys. Relatively low stacking fault energies and phase stability of the γ′ phase compared with those in Ni-base alloys are responsible for the unique deformation behaviors observed in Co-base γ′ and γ + γ′ alloys. Controlling energies of planar defects, such as stacking faults and antiphase boundaries, by alloying is critical for alloy development. Experimental and density functional theory studies indicate that additions of Ta, Ti, Nb, Hf, and Ni are effective in simultaneously increasing the phase stability and stacking fault energy of γ′-Co3(Al,W), thus improving the high-temperature strength of Co-bas.
Effector‐induced self‐association and conformational changes in the enhancer‐binding protein NTRC

The Klebsiella pneumoniae nitrogen regulatory protein NTRC is a response regulator which activates transcription in response to nitrogen limitation, and is a member of the family of σN‐dependent enhancer‐binding proteins. Using limited trypsin digestion, two domains of NTRC were detected and conformational changes within the protein in response to the binding of ligands were also observed. In the absence of ligands, the major digestion products were 42, 36 and 12.5 kDa bands corresponding to the central plus C‐terminal domain, the central domain, and the N‐terminal domains, respectively. Upon binding of purine but not pyrimidine nucleotides, the 36 kDa band was insensitive to further proteolysis, indicative of a conformational change in the central domain. Analysis of the dependence of this insensitivity on ATPγS concentration suggested an apparent dissociation constant (Kd) for ATPγS of 150 μM. In the presence of DNA, both the central and C‐terminal domains of NTRC were insensitive to proteolytic cleavage, indicative of a further conformational change. NTRC S160F, a mutant form of NTRC that is active in the absence of phosphorylation, was more stable to proteolysis than the wild‐type protein. This mutant protein is apparently locked in a conformation resembling the DNA‐bound form of wild‐type NTRC. The involvement of ligands in self‐association was studied using sedimentation equilibrium analysis. In the absence of ligand, wild‐type NTRC displayed a monomer–dimer equilibrium with a Kd of 6 μM. In the presence of ATPγS the equilibrium was shifted towards the dimer form (Kd = 0.8 μM). A similar dissociation constant for the monomer–dimer interaction was observed with NTRC S160F in the absence of ATPγS (Kd = 0.5 μM). The addition of ATPγS induced a significant association of NTRC S160F to higher‐order states with a dimer–octamer model producing a slightly, but not significantly better fit to the data than a dimer–hexamer model. We propose that ligand‐mediated self‐association provides a common mechanism for activation of this class of transcriptional regulatory proteins.
Next-generation probes, particles, and proteins for neural interfacing

Multimodal and multidisciplinary approaches lead to next-generation technologies for reading and modulating neural function. Bidirectional interfacing with the nervous system enables neuroscience research, diagnosis, and therapy. This two-way communication allows us to monitor the state of the brain and its composite networks and cells as well as to influence them to treat disease or repair/restore sensory or motor function. To provide the most stable and effective interface, the tools of the trade must bridge the soft, ion-rich, and evolving nature of neural tissue with the largely rigid, static realm of microelectronics and medical instruments that allow for readout, analysis, and/or control. In this Review, we describe how the understanding of neural signaling and material-tissue interactions has fueled the expansion of the available tool set. New probe architectures and materials, nanoparticles, dyes, and designer genetically encoded proteins push the limits of recording and stimulation lifetime, localization, and specificity, blurring the boundary between living tissue and engineered tools. Understanding these approaches, their modality, and the role of cross-disciplinary development will support new neurotherapies and prostheses and provide neuroscientists and neurologists with unprecedented access to the brain.
The Hidden Effects of Dairy Farming on Public and Environmental Health in the Netherlands, India, Ethiopia, and Uganda, Considering the Use of Antibiotics and Other Agro-chemicals

The current and expected growth of the world’s population warrants an increased production of high-quality animal protein. Dairy farming is regarded as one of the important ways of satisfying this need to meet the growing demand for milk, especially in developing countries. The focus on crossbreeding and increasing the productivity of dairy cattle has, besides enhanced milk production, also resulted in an increased use of agro-chemicals, mainly antibiotics and anti-parasite drugs. The residues of these agro-chemicals, if not managed properly, could leak into the environment, affecting natural processes, biodiversity, and soil life. Public health can also be affected due to residues in milk and meat, especially in countries with insufficient food quality controls. These processes contribute to the growing global threat to human and animal health posed by multi-resistant microbes. This article discusses the differences and similarities of dairy farming, and the effect on public and environmental health, between the Netherlands, India, Ethiopia, and Uganda, emphasizing the strategies that have been developed during the E-Motive exchange project to reduce the use of antibiotics and other chemicals in dairy farming. Proposed solutions include raising consciousness about the risk of antibiotics and their effect on food quality, and implementing the Natural Livestock Farming five-layer approach for reducing the use of antibiotics and other chemicals. This approach is based on improving animal and farm management, revitalizing ethno veterinary knowledge and the use of medicinal plants, genetic improvement through strategic use of local breeds, establishing quality control systems in the dairy chain, and extra payment to farmers for residue-free milk.
Cerebral networks for number processing: Evidence from a case of posterior callosal lesion

Abstract We report a study of number processing in a patient with a lesion selectively destroying the posterior half of her corpus callosum. This case provided an opportunity to study the cerebral distribution of numerical abilities across hemispheres, and their interhemispheric communication pathways. Tasks of interhemispheric same-different judgement with digits and sets of dots showed that exact digit identity could not be transferred between hemispheres, but that some approximate magnitude information could. With arabic numerals presented in the left visual field, reading aloud and arithmetic were severely impaired. In contrast, larger-smaller magnitude comparison was spared. With right-visual-field stimuli, the patient's performance was essentially normal in reading aloud, arithmetic and number comparison. These findings lend support to the hypothesis that both hemispheres are capable of identifying arabic digits, and of accessing and comparing the corresponding magnitudes. However, the verbal abilit.
Cluster-based fusion of retrieved lists

Methods for fusing document lists that were retrieved in response to a query often use retrieval scores (or ranks) of documents in the lists. We present a novel probabilistic fusion approach that utilizes an additional source of rich information, namely, inter-document similarities. Specifically, our model integrates information induced from clusters of similar documents created across the lists with that produced by some fusion method that relies on retrieval scores (ranks). Empirical evaluation shows that our approach is highly effective for fusion. For example, the performance of our model is consistently better than that of the standard (effective) fusion method that it integrates. The performance also transcends that of standard fusion of re-ranked lists, where list re-ranking is based on clusters created from documents in the list.
Innovative Capability and Financing Constraints for Innovation: More Money, More Innovation?

Abstract This study presents a novel empirical approach to identify financing constraints for innovation based on the concept of an ideal test (Hall, 2008). Firms were offered a hypothetical payment and asked to choose between alternatives of use. If they selected additional innovation projects, they must have had some unexploited investment opportunities that were not profitable using more costly external finance. We attribute constraints for innovation not only to lacking financing, but also to firms' innovative capability. Econometric results show that financial constraints do not depend on the availability of internal funds per se but that they are driven by innovative capability.
Clinical factors contributing to the differential diagnosis of primary insomnia and insomnia related to mental disorders.

OBJECTIVE Primary insomnia and insomnia related to mental disorders are the two most common DSM-IV insomnia diagnoses, but distinguishing between them is difficult in clinical practice. This analysis was performed to identify clinical factors used by sleep specialists to distinguish primary insomnia from insomnia related to mental disorders. METHOD Clinicians evaluated 216 patients referred for insomnia at five clinical sites, rated a list of clinical factors judged to contribute to each patient's presentation, and assigned diagnoses. Analysis of variance was performed, with contributing factors as the dependent variable and diagnostic group and clinic location as independent variables. RESULTS Sleep specialists rated a psychiatric disorder as a stronger factor for insomnia related to mental disorders and rated negative conditioning and sleep hygiene as stronger factors for primary insomnia. However, a psychiatric disorder was rated as a contributing factor for 77% of patients who received a first diagnosis of primary insomnia. CONCLUSIONS While neither sleep hygiene nor negative conditioning is a diagnostic criterion in DSM-IV, these results support the face validity of these clinical factors distinguishing between primary insomnia and insomnia related to mental disorders. The use of a psychiatric disorder as an inclusion criterion for insomnia related to mental disorders and an exclusion criterion for primary insomnia reinforces a categorical distinction between the two diagnoses, but the contribution of psychiatric symptoms in primary insomnia appears to be a clinically relevant one. These findings suggest the need for studies on the validity of negative conditioning and sleep hygiene in the etiology of primary insomnia, as well as on the significance of psychiatric disorders, especially depression, in primary insomnia.
Discrete Cortical Infarction With Prominent Impairment of Thumb Flexion

Background Intracortical efferent zones in the primary motor cortex for thumb movements, namely thumb flexion, extension, adduction, and abduction, have been described in Maccaca mullata monkeys but not in humans. Even recent cortical mapping based on intraoperative monitoring does not provide information about intracortical efferent zones as it is not ethically possible to search the human motor cortex extensively by punctate electrodes. Case Description A 78-year-old man with discrete cortical embolism over the left central sulcus is described. Only a mild weakness of his right thumb was observed. Thumb flexion was affected to a greater degree than thumb extension, adduction, and abduction. The lesion ran along the bottom of the central sulcus and affected part of the precentral and postcentral gyri on both sides of it. Animal studies in Maccaca mullata monkeys have shown that the intracortical efferent zones for thumb movement, especially for thumb flexion, are located in the part of the motor cortex just adjoining the central sulcus that folds down from the “bank” to the depth of the central sulcus. It was possible to explain the prominent weakness of thumb flexion if we applied the results of the animal studies. Conclusions Our case suggests that the same arrangement of intracortical efferent zones found in monkeys may also exist in human beings.
Plasmodium falciparum malaria transmission‐blocking immunity under conditions of low endemicity as in Sri Lanka

Sera from acute primary Plasmodium falciparum patients in Sri Lanka were tested for the presence of antibodies against gamete antigens and for their functional effects of transmission blocking activity. Comparisons were made with corresponding data from a previous study from sera of patients from Papua New Guinea where malaria is more highly endemic. Although the prevalence of anti‐gamate antibodies in the two groups were broadly similar, the prevalence of infectivity suppressive effects in the Sri Lankan sera (56%) was less than in Papua New Guinea sera (75%), suggesting that the generation of functionally effective transmission blocking antibodies requires prolonged exposure to multiple inoculations of malaria. In Papua New Guinea sera there was a good correlation between transmission blocking effects and antibody responses to Pfs 230, a known target of transmission blocking antibodies. Among the Sri Lankan sera no strong correlation was found between transmission blocking effects and the presence of antibodies to gamete surface antigens Pfs 230 nor Pfs 48/45 as detected by immunoprecipitation of radio‐iodinated gamate proteins; a strong correlation was however, found between the intensity of response to gamete surface antigens by IFA and transmission blocking effects of these sera. It is possible therefore, that the antigens identified by IFA include non‐protein moieties and that these may be the targets of transmission blocking antibodies in sera from acute primary infections of P. falciparum.
Computing approximate GCD of univariate polynomials

In this paper we discuss the problem of computing the approximate GCD of two univariate polynomials. We construct a linearly structured resultant matrix from given polynomials. We show the equivalence of the full rank property of this resultant matrix and the coprimeness of the polynomials. Further we show that the nearest structured low rank approximation (SLRA) of the resultant matrix gives the approximate GCD of the polynomials. We formulate the problem of computing the nearest SLRA as an optimization problem on a smooth manifold, namely the unit sphere SN−1 in RN.
Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples

Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells.
Urine testing to monitor the impact of HPV vaccination in Bhutan and Rwanda

Bhutan (2010) and Rwanda (2011) were the first countries in Asia and Africa to introduce national, primarily school‐based, human papillomavirus (HPV) vaccination programmes. These target 12 year‐old girls and initially included catch‐up campaigns (13–18 year‐olds in Bhutan and ninth school grade in Rwanda). In 2013, to obtain the earliest indicators of vaccine effectiveness, we performed two school‐based HPV urine surveys; 973 female students (median age: 19 years, 5th‐95th percentile: 18–22) were recruited in Bhutan and 912 (19 years, 17–20) in Rwanda. Participants self‐collected a first‐void urine sample using a validated protocol. HPV prevalence was obtained using two PCR assays that differ in sensitivity and type spectrum, namely GP5+/GP6+ and E7‐MPG. 92% students in Bhutan and 43% in Rwanda reported to have been vaccinated (median vaccination age = 16, 5th–95th: 14–18). HPV positivity in urine was significantly associated with sexual activity measures. In Rwanda, HPV6/11/16/18 prevalence was lower in vaccinated than in unvaccinated students (prevalence ratio, PR = 0.12, 95% confidence interval, CI: 0.03–0.51 by GP5+/GP6+, and 0.45, CI: 0.23–0.90 by E7‐MPG). For E7‐MPG, cross‐protection against 10 high‐risk types phylogenetically related to HPV16 or 18 was of borderline significance (PR = 0.68; 95% CI: 0.45–1.01). In Bhutan, HPV6/11/16/18 prevalence by GP5+/GP6+ was lower in vaccinated than in unvaccinated students but CIs were broad. In conclusion, our study supports the feasibility of urine surveys to monitor HPV vaccination and quantifies the effectiveness of the quadrivalent vaccine in women vaccinated after pre‐adolescence. Future similar surveys should detect increases in vaccine effectiveness if vaccination of 12 year‐olds continues.
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking

MOTIVATION Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However, incorporation of the latter terms varies a lot between existing methods, and together with many examples of distant relations not recognized even by the best methods, suggests that further improvements are still possible. RESULTS Here we describe recent improvements to the fold and function assignment system (FFAS) method, including adding optimized structural features (experimental or predicted), 'symmetrical' Z-score calculation and re-ranking the templates with a neural network. The alignment accuracy in the new FFAS-3D is now 11% higher than the original and comparable with the most accurate template-based structure prediction algorithms. At the same time, FFAS-3D has high success rate at the Structural Classification of Proteins (SCOP) family, superfamily and fold levels. Importantly, FFAS-3D results are not highly correlated with other programs suggesting that it may significantly improve meta-predictions. FFAS-3D does not require 3D structures of the templates, as using predicted features instead of structure-derived does not lead to the decrease of accuracy. Because of that, FFAS-3D can be used for databases other than Protein Data Bank (PDB) such as Protein families database or Clusters of orthologous groups thus extending its applications to functional annotations of genomes and protein families. AVAILABILITY AND IMPLEMENTATION FFAS-3D is available at http://ffas.godziklab. org.