Miracle-dz/UniFAR-FTUs huggingface dataset:
Aspergillus fumigatus High Osmolarity Glycerol Mitogen Activated Protein Kinases SakA and MpkC Physically Interact During Osmotic and Cell Wall Stresses

Aspergillus fumigatus, a saprophytic filamentous fungus, is a serious opportunistic pathogen of mammals and it is the primary causal agent of invasive aspergillosis (IA). Mitogen activated protein Kinases (MAPKs) are important components involved in diverse cellular processes in eukaryotes. A. fumigatus MpkC and SakA, the homologs of the Saccharomyces cerevisiae Hog1 are important to adaptations to oxidative and osmotic stresses, heat shock, cell wall damage, macrophage recognition, and full virulence. We performed protein pull-down experiments aiming to identify interaction partners of SakA and MpkC by mass spectrometry analysis. In presence of osmotic stress with sorbitol, 118, and 213 proteins were detected as possible protein interactors of SakA and MpkC, respectively. Under cell wall stress caused by congo red, 420 and 299 proteins were detected interacting with SakA and MpkC, respectively. Interestingly, a group of 78 and 256 proteins were common to both interactome analysis. Co-immunoprecipitation (Co-IP) experiments showed that SakA::GFP is physically associated with MpkC:3xHA upon osmotic and cell wall stresses. We also validated the association between SakA:GFP and the cell wall integrity MAPK MpkA:3xHA and the phosphatase PtcB:3xHA, under cell wall stress. We further characterized A. fumigatus PakA, the homolog of the S. cerevisiae sexual developmental serine/threonine kinase Ste20, as a component of the SakA/MpkC MAPK pathway. The ΔpakA strain is more sensitive to cell wall damaging agents as congo red, calcofluor white, and caspofungin. Together, our data supporting the hypothesis that SakA and MpkC are part of an osmotic and general signal pathways involved in regulation of the response to the cell wall damage, oxidative stress, drug resistance, and establishment of infection. This manuscript describes an important biological resource to understand SakA and MpkC protein interactions. Further investigation of the biological roles played by these protein interactors will provide more opportunities to understand and combat IA.
Mouse Models and Online Resources for Functional Analysis of Osteoporosis Genome-Wide Association Studies

Osteoporosis is a complex genetic disease in which the number of loci associated with the bone mineral density, a clinical risk factor for fracture, has increased at an exponential rate in the last decade. The identification of the causative variants and candidate genes underlying these loci has not been able to keep pace with the rate of locus discovery. A large number of tools and data resources have been built around the use of the mouse as model of human genetic disease. Herein, we describe resources available for functional validation of human Genome Wide Association Study (GWAS) loci using mouse models. We specifically focus on large-scale phenotyping efforts focused on bone relevant phenotypes and repositories of genotype-phenotype data that exist for transgenic and mutant mice, which can be readily mined as a first step toward more targeted efforts designed to deeply characterize the role of a gene in bone biology.
Optimal Resampling for Learning Small Models

Models often need to be constrained to a certain size for them to be considered interpretable, for e.g., a decision tree of depth 5 is much easier to make sense of than one of depth 30. This suggests a trade-off between interpretability and accuracy. Our work tries to minimize this trade-off by suggesting the optimal distribution of the data to learn from, that surprisingly, may be different from the original distribution. We use an Infinite Beta Mixture Model (IBMM) to represent a specific set of sampling schemes. The parameters of the IBMM are learned using a Bayesian Optimizer (BO). While even under simplistic assumptions a distribution in the original $d$-dimensional space would need to optimize for $O(d)$ variables - cumbersome for most real-world data - our technique lowers this number significantly to a fixed set of 8 variables at the cost of some additional preprocessing. The proposed technique is \emph{model-agnostic}; it can be applied to any classifier. It also admits a general notion of model size. We demonstrate its effectiveness using multiple real-world datasets to construct decision trees, linear probability models and gradient boosted models.
Does inability to allocate attention contribute to balance constraints during gait in older adults?

BACKGROUND Recent research has explored dual-task deficits during locomotion in older adults, yet the mechanisms underlying these deficits are poorly understood. In the current study, we examined one possible factor contributing to these deficits, the inability to flexibly allocate attention between two tasks. METHODS Twelve healthy young adults and 12 healthy elderly adults performed obstacle avoidance while walking and an auditory Stroop task either alone or simultaneously. RESULTS Using an attentional allocation index (AAI) to compare performance of healthy young and older adults and to measure the flexibility of allocation of attention, results showed a tendency in older adults toward a decreased ability to flexibly allocate their attention between the two tasks, with small AAI values. The decreased ability to allocate attention in older adults was found to be more prominent in the auditory Stroop task performance than in the obstacle avoidance task. CONCLUSION This study suggests that an important factor contributing to decreased dual-task performance in older adults when simultaneously performing a postural and secondary cognitive task is a reduced ability to flexibly allocate attention between the two tasks, with the general ability to switch attention flexibly being predictive of the ability to adhere to a prioritized focus.
Feature Extraction and Selection for Pain Recognition Using Peripheral Physiological Signals

In pattern recognition, the selection of appropriate features is paramount to both the performance and the robustness of the system. Over-reliance on machine learning-based feature selection methods can, therefore, be problematic; especially when conducted using small snapshots of data. The results of these methods, if adopted without proper interpretation, can lead to sub-optimal system design or worse, the abandonment of otherwise viable and important features. In this work, a deep exploration of pain-based emotion classification was conducted to better understand differences in the results of the related literature. In total, 155 different time domain and frequency domain features were explored, derived from electromyogram (EMG), skin conductance levels (SCL), and electrocardiogram (ECG) readings taken from the 85 subjects in response to heat-induced pain. To address the inconsistency in the optimal feature sets found in related works, an exhaustive and interpretable feature selection protocol was followed to obtain a generalizable feature set. Associations between features were then visualized using a topologically-informed chart, called Mapper, of this physiological feature space, including synthesis and comparison of results from previous literature. This topological feature chart was able to identify key sources of information that led to the formation of five main functional feature groups: signal amplitude and power, frequency information, nonlinear complexity, unique, and connecting. These functional groupings were used to extract further insight into observable autonomic responses to pain through a complementary statistical interaction analysis. From this chart, it was observed that EMG and SCL derived features could functionally replace those obtained from ECG. These insights motivate future work on novel sensing modalities, feature design, deep learning approaches, and dimensionality reduction techniques.
Cdc42 Effector Protein 3 Interacts With Cdc42 in Regulating Xenopus Somite Segmentation

Somitogenesis is a critical process during vertebrate development that establishes the segmented body plan and gives rise to the vertebra, skeletal muscles, and dermis. While segmentation clock and wave front mechanisms have been elucidated to control the size and time of somite formation, regulation of the segmentation process that physically separates somites is not understood in detail. Here, we identified a cytoskeletal player, Cdc42 effector protein 3 (Cdc42ep3, CEP3) that is required for somite segmentation in Xenopus embryos. CEP3 is specifically expressed in somite tissue during somite segmentation. Loss-of-function experiments showed that CEP3 is not required for the specification of paraxial mesoderm, nor the differentiation of muscle cells, but is required for the segmentation process. Live imaging analysis further revealed that CEP3 is required for cell shape changes and alignment during somitogenesis. When CEP3 was knocked down, somitic cells did not elongate efficiently along the mediolateral axis and failed to undertake the 90° rotation. As a result, cells remained in a continuous sheet without an apparent segmentation cleft. CEP3 likely interacts with Cdc42 during this process, and both increased and decreased Cdc42 activity led to defective somite segmentation. Segmentation defects caused by Cdc42 knockdown can be partially rescued by the overexpression of CEP3. Conversely, loss of CEP3 resulted in the maintenance of high levels of Cdc42 activity at the cell membrane, which is normally reduced during and after somite segmentation. These results suggest that there is a feedback regulation between Cdc42 and CEP3 during somite segmentation and the activity of Cdc42 needs to be fine-tuned to control the coordinated cell shape changes and movement required for somite segmentation.
Perturbation methods in control of flexible link manipulators

The resolution of the dynamics of flexible manipulators into rigid and flexible modes is considered. The decoupling is established on the single-link case by singular perturbation techniques. The flexural effects of the manipulator on its rigid-body motion are included by using the higher-order terms in the asymptotic expansion. The model used is the integro-partial-differential equation resulting from the extended Hamiltonian principle. Use of this model, rather than a finite-dimensional approximation, yields more insight and a more compact way of obtaining the higher-order terms that represent the coupling between the rigid and the flexure modes. Asymptotic perturbation techniques are utilized to generate a composite control law. <<ETX>>
On Exploring Undetermined Relationships for Visual Relationship Detection

In visual relationship detection, human-notated relationships can be regarded as determinate relationships. However, there are still large amount of unlabeled data, such as object pairs with less significant relationships or even with no relationships. We refer to these unlabeled but potentially useful data as undetermined relationships. Although a vast body of literature exists, few methods exploit these undetermined relationships for visual relationship detection. In this paper, we explore the beneficial effect of undetermined relationships on visual relationship detection. We propose a novel multi-modal feature based undetermined relationship learning network (MF-URLN) and achieve great improvements in relationship detection. In detail, our MF-URLN automatically generates undetermined relationships by comparing object pairs with human-notated data according to a designed criterion. Then, the MF-URLN extracts and fuses features of object pairs from three complementary modals: visual, spatial, and linguistic modals. Further, the MF-URLN proposes two correlated subnetworks: one subnetwork decides the determinate confidence, and the other predicts the relationships. We evaluate the MF-URLN on two datasets: the Visual Relationship Detection (VRD) and the Visual Genome (VG) datasets. The experimental results compared with state-of-the-art methods verify the significant improvements made by the undetermined relationships, e.g., the top-50 relation detection recall improves from 19.5% to 23.9% on the VRD dataset.
Learning Local RGB-to-CAD Correspondences for Object Pose Estimation

We consider the problem of 3D object pose estimation. While much recent work has focused on the RGB domain, the reliance on accurately annotated images limits generalizability and scalability. On the other hand, the easily available object CAD models are rich sources of data, providing a large number of synthetically rendered images. In this paper, we solve this key problem of existing methods requiring expensive 3D pose annotations by proposing a new method that matches RGB images to CAD models for object pose estimation. Our key innovations compared to existing work include removing the need for either real-world textures for CAD models or explicit 3D pose annotations for RGB images. We achieve this through a series of objectives that learn how to select keypoints and enforce viewpoint and modality invariance across RGB images and CAD model renderings. Our experiments demonstrate that the proposed method can reliably estimate object pose in RGB images and generalize to object instances not seen during training.
Systemic Sclerosis (Scleroderma): Specific Autoantigen Genes Are Selectively Overexpressed in Scleroderma Fibroblasts1

The pathogenesis of systemic sclerosis (SSc) involves complex interactions between activated fibroblasts eventually leading to fibrosis, and impaired immune tolerance characterized by a variety of circulating SSc-specific autoantibodies. The expression of autoantigens in fibroblasts, a key target tissue in SSc, may play an important role in this process. To obtain a global view of this process, we examined gene expression profiles of SSc dermal fibroblasts using cDNA microarrays. The results show that dermal fibroblasts from SSc patients obtained from either affected or unaffected skin displayed a characteristic pattern of increased SSc autoantigen gene expression compared with that from normal controls. In particular, fibrillarin (p = 0.028), centromeric protein B (p = 0.01), centromeric autoantigen P27 (p = 0.042), and RNA polymerase II (220 kDa; p = 0.02) were significantly overexpressed in SSc fibroblasts. Quantitative RT-PCR confirmed overexpression of these autoantigens and also revealed increased levels of DNA topoisomerase I transcripts in SSc fibroblasts compared with normal control fibroblasts (p = 0.0318). The polymyositis/scleroderma autoantigen gene was overexpressed in some SSc patients (p = 0.09). To examine the specificity of these overexpressed autoantigen genes for SSc and its tissue specificity for fibroblasts, cDNA microarrays of dermal fibroblasts from patients with eosinophilic fasciitis and scleromyxedema were studied as well as PBMC and muscle biopsies from SSc patients. None of these tissues showed significant alterations in gene expression of SSc-specific autoantigens. Therefore, SSc-associated autoantigen genes are selectively overexpressed in SSc dermal fibroblasts, a major tissue involved in disease pathogenesis.
Beyond the Solar Circle − Trends in Massive Star Formation Between the Inner and Outer Galaxy

We have compiled the most complete compact and ultracompact H II region catalogue to date via multi-wavelength inspection of survey data. We utilise data from the recently available SASSy 850 µm survey to identify massive star forming clumps in the outer Galaxy (RGC > 8.5 kpc) and cross-match with infrared and radio data of known UC H II regions from the RMS database. For the inner Galaxy sample (RGC < 8.5 kpc), we adopt the compact H II regions from previous works that used similar methods to cross match ATLASGAL with either CORNISH or RMS, depending on the location within the Galactic plane. We present a new UC H II region catalogue that more than doubles the original sample size of previous work, totalling 536 embedded H II regions and 445 host clumps. We examine the distance independent values of NLy/M and Lbol/M as proxies for massive star formation efficiency and overall star formation efficiency, respectively. We find a significant trend showing that Lbol/M decreases with increasing RGC, suggesting that the overall star formation per unit mass is less in the outer Galaxy.
Low Noise Amplifier for the MICS band in CMOS 180 nm Technology

The main focus of this paper is to design a Low Noise Amplifier for the Medical Implant Communication Services (MICS) band. Low Noise Amplifier (LNA) is designed by utilizing the techniques of current-reuse, feedback and back gate coupling. Both nMOS and pMOS transistors are used to save power consumption and to enhance gain, common gate (CG) and Shunt feedback (SFB) topologies are combined. LNA achieves 10dB of Gain, 11.6dB Noise figure and -18dBm of IIP3. Simulations are done using H-SPICE in CMOS 180nm PTM Technology.
CBF1 controls the retinotectal topographical map along the anteroposterior axis through multiple mechanisms

Chick brain factor 1 (CBF1), a nasal retina-specific winged-helix transcription factor, is known to prescribe the nasal specificity that leads to the formation of the precise retinotectal map, especially along the anteroposterior (AP) axis. However, its downstream topographic genes and the molecular mechanisms by which CBF1 controls the expression of them have not been elucidated. We show that misexpression of CBF1 represses the expression of EphA3 and CBF2, and induces that of SOHo1, GH6, ephrin A2 and ephrin A5. CBF1 controls ephrin A5 by a DNA binding-dependent mechanism, ephrin A2 by a DNA binding-independent mechanism, and CBF2, SOHo1, GH6 and EphA3 by dual mechanisms. BMP2 expression begins double-gradiently in the retina from E5 in a complementary pattern to Ventroptin expression. Ventroptin antagonizes BMP2 as well as BMP4. CBF1 interferes in BMP2 signaling and thereby induces expression of ephrin A2. Our data suggest that CBF1 is located at the top of the gene cascade for the regional specification along the nasotemporal (NT) axis in the retina and distinct BMP signals play pivotal roles in the topographic projection along both axes.
The (In)Significance of Race and Discrimination among Latino Youth: The Case of Depressive Symptoms

Abstract Despite the growing population of Latinos in the United States, there is little research that explores how discrimination affects the mental health of Latino youth along racial lines. In this paper we ask two closely related questions. First, do black Latino youth have higher or lower symptoms of depression than nonblack Latinos? Second, is the relationship between race and depression among Latino youth buffered by discrimination stress? Results from the Transitions Study show that black Latino youth have significantly higher symptoms of depression than nonblack Latinos. The relationship between race and depression depends on daily—but not on lifetime—experiences of discrimination. The combined effect of race and discrimination holds in the face of a wide range of measures of stress, including major lifetime events, recent life events, and chronic stressors. These findings encourage future research that considers the mental health effects of racial variation among Latinos.
Does stellar mass assembly history vary with environment

Using the publicly available VESPA database of SDSS Data Release 7 spectra, we calculate the stellar Mass Weighted Age (hereafter MWA) as a function of local galaxy density and dark matter halo mass. We compare our results with semi-analytic models from the public Millennium Simulation. We nd that the stellar MWA has a large scatter which is inherent in the data and consistent with that seen in semi-analytic models. The stellar MWA is consistent with being independent (to rst order) with local galaxy density, which is also seen in semi-analytic models. As a function of increasing dark matter halo mass (using the SDSS New York Value Added Group catalogues), we nd that the average stellar MWA for member galaxies increases, which is again found in semi-analytic models. Furthermore we use public dark matter Mass Accretion History (MAH) code calibrated on simulations, to calculate the dark matter Mass Weighted Age as a function of dark matter halo mass. In agreement with earlier analyses, we nd that the stellar MWA and the dark matter MWA are anti correlated for large mass halos, i.e, dark matter accretion does not seem to be the primary factor in determining when stellar mass was compiled. This eect can be described by down-sizing.
PROGRESSION IN STUDENT CREATIVITY IN SCHOOL: FIRST STEPS TOWARDS NEW FORMS OF FORMATIVE ASSESSMENTS

Creativity is widely accepted as being an important outcome of schooling. Yet there are many different views about what it is, how best it can be cultivated in young people and whether or how it should be assessed. And in many national curricula creativity is only implicitly acknowledged and seldom precisely defined. This paper offers a five dimensional definition of creativity which has been trialled by teachers in two field trials in schools in England. The paper suggests a theoretical underpinning for defining and assessing creativity along with a number of practical suggestions as to how creativity can be developed and tracked in schools. Two clear benefits of assessing progress in the development of creativity are identified: 1) teachers are able to be more precise and confident in developing young people’s creativity, and 2) learners are better able to understand what it is to be creative (and to use this understanding to record evidence of their progress). The result would seem to be a greater likelihood that learners can display the full range of their creative dispositions in a wide variety of contexts. La creativite est largement acceptee comme etant un resultat scolaire important. Pourtant il y a beaucoup d’opinions differentes sur ce qu’elle est, comment on peut la cultiver chez les jeunes gens, et si et comment on devrait l’evaluer. De plus, dans beaucoup de programmes scolaires, la creativite n’est reconnue que de maniere implicite et rarement definie de maniere precise. Ce document offre une definition de la creativite reposant sur cinq dimensions, qui a ete testee par des enseignants durant deux experiences de terrain dans des ecoles en Angleterre. Le document propose un soubassement theorique pour definir et evaluer la creativite ainsi que nombre de suggestions pratiques sur le developpement et le suivi de la creativite a l’ecole. Deux benefices clairs d’evaluer le progres dans le developpement de la creativite sont identifies : 1) les enseignants peuvent etre plus precis et confiants lorsqu’ils developpent la creativite des jeunes gens, et 2) les apprenants sont davantage en mesure de comprendre ce que « etre creatif » signifie (et a utiliser cette comprehension pour documenter et relater leur progres). Le resultat semble etre une plus grande probabilite que les apprenants temoignent de toute l’etendue de leurs dispositions a la creativite dans un large eventail de contextes.
Glutathione S-transferase T1 and myeloperoxidase −463 G>A genotypes in lung cancer patients of Kumaun region

Background: Null genetic polymorphism of Glutathione S-transferase T1 (GSTT1) and -463 G>A promoter polymorphism of myeloperoxidase (MPO) were studied for association with lung cancer. Materials and Methods: In a case- control study 26 lung cancer patients and 33 healthy individuals from hilly Kumaun region of northern India were investigated. DNA was extracted from peripheral blood. GSTT1 null polymorphism was detected by duplex PCR, and MPO polymorphism was detected by performing PCR-RFLP. Results: An increased but statistically non- significant risk for lung cancer was found for GSTT1 null genotype. No association for MPO -463G>A genotype was evident. Conclusion: Further study with large sample size may reveal such association in this population.