Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucose removal from N-linked oligosaccharides is required for efficient maturation of certain secretory glycoproteins from the rough endoplasmic reticulum to the Golgi complex

1- Deoxynojirimycin is a specific inhibitor of glucosidases I and II, the first enzymes that process N-linked oligosaccharides after their transfer to polypeptides in the rough endoplasmic reticulum. In a pulse- chase experiment, 1- deoxynojirimycin greatly reduced the rate of secretion of alpha 1-antitrypsin and alpha 1-antichymotrypsin by human hepatoma HepG2 cells, but had marginal effects on secretion of the glycoproteins C3 and transferrin, or of albumin. As judged by equilibrium gradient centrifugation, 1- deoxynojirimycin caused alpha 1- antitrypsin and alpha 1-antichymotrypsin to accumulate in the rough endoplasmic reticulum. The oligosaccharides on cell-associated alpha 1- antitrypsin and alpha 1-antichymotrypsin synthesized in the presence of 1- deoxynojirimycin , remained sensitive to Endoglycosidase H and most likely had the structure Glu1- 3Man9GlcNAc2 . Tunicamycin, an antibiotic that inhibits addition of N-linked oligosaccharide units to glycoproteins, had a similar differential effect on secretion of these proteins. Swainsonine , an inhibitor of the Golgi enzyme alpha- mannosidase II, had no effect on the rates of protein secretion, although the proteins were in this case secreted with an abnormal N- linked, partially complex, oligosaccharide. We conclude that the movement of alpha 1-antitrypsin and alpha 1-antichymotrypsin from the rough endoplasmic reticulum to the Golgi requires that the N-linked oligosaccharides be processed to at least the Man9GlcNAc2 form; possibly this oligosaccharide forms part of the recognition site of a transport receptor for certain secretory proteins.
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, and removing the majority of errors. Digital normalization substantially reduces the size of shotgun data sets and decreases the memory and time requirements for {\em de novo} sequence assembly, all without significantly impacting content of the generated contigs. We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification.
Smooth B-spline illumination maps for bidirectional ray tracing

In this paper we introduce B-spline illumination maps and their generalizations and extensions for use in realistic image generation algorithms. The B-spline lighting functions (i.e., illumination maps) are defined as weighted probability density functions. The lighting functions can be estimated from random data and may be used in bidirectional distributed ray tracing programs as well as radiosity oriented algorithms. The use of these lighting functions in a bidirectional ray tracing system that can handle dispersion as well as the focusing of light through lenses is presented.
Human-like gradual multi-agent Q-learning using the concept of behavior-based robotics for autonomous exploration

In the last few years, the field of mobile robotics has made lots of advancements. These advancements are due to the extensive application of mobile robots for autonomous exploration. Mobile robots are being popularly used for applications in space, underwater explorations, underground coal mines monitoring, inspection in chemical/toxic/ nuclear factories etc. But if these environments are unknown/unpredictable, conventional/ classical robotics may not serve the purpose. In such cases robot learning is the best option. Learning from the past experiences, is one such way for real time application of robots for completely unknown environments. Reinforcement learning is one of the best learning methods for robots using a constant system-environment interaction. Both single and multi-agent concepts are available for implementation of learning. The current research work describes a multi-agent based reinforcement learning using the concept of behaviour-based robotics for autonomous exploration of mobile robots. The concept has also been tested both in indoor and outdoor environments using real-time robots.
MiR-143 acts as a tumor suppressor by targeting N-RAS and enhances temozolomide-induced apoptosis in glioma

Therapeutic applications of microRNAs (miRNAs) in RAS-driven glioma were valuable, but their specific roles and functions have yet to be fully elucidated. Here, we firstly report that miR-143 directly targets the neuroblastoma RAS viral oncogene homolog (N-RAS) and functions as a tumor-suppressor in glioma. Overexpression of miR-143 decreased the expression of N-RAS, inhibited PI3K/AKT, MAPK/ERK signaling, and attenuated the accumulation of p65 in nucleus of glioma cells. In human clinical specimens, miR-143 was downregulated where an adverse with N-RAS expression was observed. Furthermore, overexpression of miR-143 decreased glioma cell migration, invasion, tube formation and slowed tumor growth and angiogenesis in a manner associated with N-RAS downregulation in vitro and in vivo. Finally, miR-143 also sensitizes glioma cells to temozolomide (TMZ),the first-line drug for glioma treatment. Taken together, for the first time, our results demonstrate that miR-143 plays a significant role in inactivating the RAS signaling pathway through the inhibition of N-RAS, which may provide a novel therapeutic strategy for treatment of glioma and other RAS-driven cancers.
Computational Studies of the Intestinal Host-Microbiota Interactome

A large and growing body of research implicates aberrant immune response and compositional shifts of the intestinal microbiota in the pathogenesis of many intestinal disorders. The molecular and physical interaction between the host and the microbiota, known as the host-microbiota interactome, is one of the key drivers in the pathophysiology of many of these disorders. This host-microbiota interactome is a set of dynamic and complex processes, and needs to be treated as a distinct entity and subject for study. Disentangling this complex web of interactions will require novel approaches, using a combination of data-driven bioinformatics with knowledge-driven computational modeling. This review describes the computational approaches for investigating the host-microbiota interactome, with emphasis on the human intestinal tract and innate immunity, and highlights open challenges and existing gaps in the computation methodology for advancing our knowledge about this important facet of human health.
Spectral-domain optical coherence tomography evaluation of the cornea, retina, and optic nerve in normal horses.

PURPOSE To determine the feasibility of using a handheld spectral-domain optical coherence tomography (SD-OCT) instrument to characterize normal corneal, retinal, and optic nerve head anatomy in vivo in standing horses. METHODS Clinically normal horses under sedation, palpebral nerve blockage, and pharmacologically induced mydriasis were imaged with a SD-OCT instrument (Envisu SD-OCT, Bioptigen, Inc., Morrisville, NC). Radial volumes from the cornea (axial, superior, inferior, nasal, and temporal), and rectangular volumes from the retina (dorsal, ventral, nasal, and temporal) and optic nerve head were acquired. Manual measurements of the corneal layers within the five regions, retinal and nerve fiber layer thickness in the four different regions adjacent to the ONH, and vertical and horizontal axis of the optic nerve head (ONH) and optic cup (OC) were obtained using the same device. RESULTS Total corneal thickness (mean ± SD) measurements were 800 ± 50, 937 ± 61, 956 ± 61, 912 ± 65, and 884 ± 68 μm for the axial, superior, inferior, nasal, and temporal regions, respectively. The highest total retinal and nerve fiber layer thickness (mean ± SD), at the level of the ONH, was found nasally 459 ± 115 and 377 ± 116 μm, respectively, followed by the temporal, dorsal, and ventral quadrants. The dimensions of the ONH and OC (mean ± SD) were 3.682 ± 0.276 and 2.175 ± 0.502 mm for the horizontal, and 3.012 ± 0.278 and 2.035 ± 0.488 mm for the vertical axis. CONCLUSIONS The SD-OCT instrument employed in this study may be used on sedated horses and allows the acquisition of high-resolution images, and thickness measurements involving the cornea, retina, and optic nerve.
Object Transaction Service: experiences and open issues

Transaction management is required to maintain data consistency in any system with concurrent access to its information. The Object Transaction Service (OTS) is a CORBA service that brings transactional semantics to distributed object oriented applications. We report our experience of developing a prototype using OTS. We present results from our scaling experiments and analyze the overheads incurred by the components of an OTS based distributed transaction. We also highlight issues that need to be addressed if OTS is to be used in large distributed systems such as those in Boeing.
No evidence for higher risk of cancer in patients with multiple sclerosis taking cladribine

Objective: To compare the cancer risk of cladribine and other disease-modifying drugs (DMDs) in trials of people with relapsing multiple sclerosis (pwRMS). Methods: Meta-analysis of phase III trials of licensed DMDs for pwRMS and a phase III trial of cladribine (CLARITY). Cancer rates were compared using Fisher exact test. Results: Eleven trials were included. Investigated treatments included cladribine, dimethyl fumarate, fingolimod, teriflunomide, natalizumab, alemtuzumab, and glatiramer acetate. The cancer rate in the CLARITY treatment group (0.34%) was not increased compared to all other treatment groups, whether including placebo-controlled trials only (0.6%, p = 0.4631) or all trials, i.e., including those with an active comparator arm (0.67%, p = 0.3669). No cancer was reported in the CLARITY placebo group, whereas the combined cancer rate of all other placebo groups was 1.19% (p = 0.0159). The cancer rate of zero in the CLARITY placebo group was also lower than that in the phase III trial of cladribine in people with clinically isolated syndrome (ORACLE MS, 2.91%, p = 0.0012). In fact, no difference was detected between cancer rates in the treatment groups of CLARITY (0.34%) and ORACLE MS (0.49%) (p = 0.6546). Conclusions: Our study does not support an increased cancer risk from cladribine in the doses used in CLARITY and ORACLE MS, which previously contributed to refusal of market authorization of cladribine in Europe. Longer-term follow-up is required to assess the safety profile of cladribine, as well as currently licensed DMDs, to definitively assess cancer risk.
Geometrical pattern effect on silicon deep etching by an inductively coupled plasma system

The etching rate in silicon deep reactive ion etching (RIE) is related to pattern geometry and a frequently seen defect, RIE lag, appears in feature sizes up to hundreds of micrometers. Different feature dimensions of rectangles, squares and circles/doughnuts are designed to realize how the geometrical pattern affects RIE lag in the inductively coupled plasma (ICP) etching process. Experimental results reveal that the primary dominating factor in RIE lag is feature width and secondary factors are feature area, shape and length-to-width ratio. Etching rates of rectangular trenches are sensitive to width while ring trenches are sensitive to both width and area. Process parameters are also adjusted to control RIE lag magnitude and realize its mechanism. The inverse RIE lag phenomenon appears at a much higher pressure of APC (auto pressure control) 75% at constant area features. The formation and removal of passivation film at the trench bottom will delay Si etching by F radical density, which will start earlier in a small width than a large one. It will be more obvious at higher pressure and lead to the reduction of RIE lag. This indicates that the cause of RIE lag in ICP etching is primarily attributed to the formation and removal of passivation film at the bottom of the trench, together with feature geometry. The RIE lag-eliminated trenches with constant area are obtained at a higher pressure of APC 70%. Deep and high aspect ratio silicon microstructures can be controlled by ICP etching with different pattern geometry.
Electrodes – the challenge in electrical characterization of biological material

Electrodes are an important part of the impedance measurement chain but their influence is often underestimated. Electrochemical reactions or polarization effects, especially for galvanically coupled systems are sometimes completely neglected. The most important features of electrodes to be considered are the geometry with respect to the structure of the material to be tested and the electrochemistry at the electrode surface. Especially drift and corrosion effects may yield misleading results. If applicable, sophisticated electrode systems should be used in order to prevent the distorting influence of electrode polarization, for extending the useful frequency range of the electrodes or for enhancing the signal-to-noise ratio.
Dropout from outpatient mental health care in the United States.

OBJECTIVE Although mental health treatment dropout is common, patterns and predictors of dropout are poorly understood. This study explored patterns and predictors of mental health treatment dropout in a nationally representative sample. METHODS Data were from the National Comorbidity Survey Replication, a nationally representative household survey. Respondents who had received mental health treatment in the 12 months before the interview (N=1,664) were asked about dropout, which was defined as quitting treatment before the provider wanted them to stop. Cross-tabulation and discrete-time survival analyses were used to identify predictors. RESULTS Approximately one-fifth (22%) of patients quit treatment prematurely. The highest dropout rate was from treatment received in the general medical sector (32%), and the lowest was from treatment received by psychiatrists (15%). Dropout rates were intermediate from treatment in the human services sector (20%) and among patients seen by nonpsychiatrist mental health professionals (19%). Over 70% of all dropout occurred after the first or second visits. Mental health insurance was associated with low odds of dropout (odds ratio=.6, 95% confidence interval=.4-.9). Psychiatric comorbidity was associated with a trend toward dropout. Several patient characteristics differentially predicted dropout across treatment sectors and in early and later phases of treatment. CONCLUSIONS Roughly one-fifth of adults in mental health treatment dropped out before completing the recommended course of treatment. Dropout was most common in the general medical sector and varied by patient characteristics across treatment sectors. Interventions focused on high-risk patients and sectors that have higher dropout rates will likely be required to reduce the large proportion of patients who prematurely terminate treatment.
Visual analysis of self-organizing maps

In the article, an additional visualization of self-organizing maps (SOM) has been investigated. The main objective of self-organizing maps is data clustering and their graphical presentation. Opportunities of SOM visualization in four systems (NeNet, SOM-Toolbox, Data- bionic ESOM and Viscovery SOMine) have been investigated. Each system has its additional tools for visualizing SOM. A comparative analysis has been made for two data sets: Fisher's iris data set and the economic indices of the European Union countries. A new SOM system is also introduced and researched. The system has a specific visualization tool. It is missing in other SOM systems. It helps to see the proportion of neurons, corresponding to the data items, belonging to the different classes, and fallen in the same SOM cell.
Uncertainty-Aware Guided Volume Segmentation

Although direct volume rendering is established as a powerful tool for the visualization of volumetric data, efficient and reliable feature detection is still an open topic. Usually, a tradeoff between fast but imprecise classification schemes and accurate but time-consuming segmentation techniques has to be made. Furthermore, the issue of uncertainty introduced with the feature detection process is completely neglected by the majority of existing approaches.In this paper we propose a guided probabilistic volume segmentation approach that focuses on the minimization of uncertainty. In an iterative process, our system continuously assesses uncertainty of a random walker-based segmentation in order to detect regions with high ambiguity, to which the user's attention is directed to support the correction of potential misclassifications. This reduces the risk of critical segmentation errors and ensures that information about the segmentation's reliability is conveyed to the user in a dependable way. In order to improve the efficiency of the segmentation process, our technique does not only take into account the volume data to be segmented, but also enables the user to incorporate classification information. An interactive workflow has been achieved by implementing the presented system on the GPU using the OpenCL API. Our results obtained for several medical data sets of different modalities, including brain MRI and abdominal CT, demonstrate the reliability and efficiency of our approach.
Transfusion-transmitted parasitic infections

The transmission of parasitic organisms through transfusion is relatively rare. Of the major transfusion-transmitted diseases, malaria is a major cause of TTIP in tropical countries whereas babesiosis and Chagas’ disease pose the greatest threat to donors in the USA In both cases, this is due to the increased number of potentially infected donors. There are no reliable serologic tests available to screen donors for any of these organisms and the focus for prevention remains on adherence to donor screening guidelines that address travel history and previous infection with the etiologic agent. One goal is the development of tests that are able to screen for and identify donors potentially infectious for parasitic infections without causing the deferral of a large number of non-infectious donors or significantly increasing costs. Ideally, methods to inactivate the infectious organism will provide an element of added safety to the blood supply.
Apoptosis Is Not Increased in Myocardium Overexpressing Type 2 Angiotensin II Receptor in Transgenic Mice

Abstract—To determine whether angiotensin type 2 (AT2) receptor stimulation induces apoptosis in cardiomyocytes in vivo, we developed transgenic mice overexpressing the AT2 receptor in a cardiac-specific manner, using the &agr;-myosin heavy-chain promoter. Ten- to 12-week-old male homozygous transgenic mice (n=44) and wild-type mice (n=44) were used. Both transgenic and wild-type mice were given either saline (control), a subpressor dose of angiotensin II (100 ng · kg−1 · min−1), a pressor dose of angiotensin II (1000 ng · kg−1 · min−1) for 14 days, a pressor dose of angiotensin II for 28 days to investigate the effects of stimulation on both angiotensin type 1 (AT1) and AT2 receptors, the AT1 antagonist L158809 alone, or a combination of angiotensin II (1000 ng · kg−1 · min−1) and L158809 for 14 days to investigate the effects of selective AT2 receptor stimulation. Apoptosis was analyzed in paraffin-embedded ventricular sections by the terminal deoxynucleotidyl-transferase-mediated dUTP nick-end labeling (TUNEL) technique. In both transgenic and wild-type mice, administration of a subpressor dose of angiotensin II, L158809, or a combination of angiotensin II and L158809 did not significantly affect the tail-cuff blood pressure or heart-to-body weight ratio, whereas administration of a pressor dose of angiotensin II for 14 or 28 days significantly increased blood pressure and the heart-to-body weight ratio. However, there was no statistical difference between the effects of angiotensin II in transgenic and wild-type mice. The number of TUNEL-positive nuclei was ≈0 to 10 per 100 000 cardiomyocytes, with no difference between transgenic and wild-type mice, regardless of saline infusion or any stimulation. In infarcted canine myocardial tissue sections for positive control, the number of TUNEL-positive nuclei was increased by 13.8 to 19.1 times compared with those in the noninfarcted myocardium. In conclusion, angiotensin II infusion for a period of 28 days failed to induce cardiomyocyte apoptosis regardless of the presence or absence of cardiac AT2 receptor overexpression. It is unlikely that in mice the AT2 receptor is a strong signal to induce cardiomyocyte apoptosis in vivo.
A systematic approach to identify cellular auxetic materials

Auxetics are materials showing a negative Poisson’s ratio. This characteristic leads to unusual mechanical properties that make this an interesting class of materials. So far no systematic approach for generating auxetic cellular materials has been reported. In this contribution, we present a systematic approach to identifying auxetic cellular materials based on eigenmode analysis. The fundamental mechanism generating auxetic behavior is identified as rotation. With this knowledge, a variety of complex two-dimensional (2D) and three-dimensional (3D) auxetic structures based on simple unit cells can be identified.
Heparan Sulfate Heterogeneity in Skeletal Muscle Basal Lamina: Demonstration by Phage Display-Derived Antibodies

The basal lamina (BL) enveloping skeletal muscle fibers contains different glycoproteins, including proteoglycans. To obtain more information on the glycosaminoglycan moiety of proteoglycans, we have selected a panel of anti-heparan sulfate (HS) antibodies from a semisynthetic antibody phage display library by panning against glycosaminoglycan preparations derived from skeletal muscle. Epitope recognition by the antibodies is strongly dependent onO- and N-sulfation of the heparan sulfate. Immunostaining with these antibodies showed a distinct distribution of heparan sulfate epitopes in muscle basal lamina of various species. Clear differences in staining intensity were observed between neural, synaptic, and extrasynaptic basal laminae. Moreover, temporal and regional changes in abundancy of heparan sulfate epitopes were observed during muscle development both in vitroand in vivo. Taken together, these data suggest a role for specific heparan sulfate domains/species in myogenesis and synaptogenesis. Detailed analysis of the functions of heparan sulfate epitopes in muscle morphogenesis has now become feasible with the isolation of antibodies specific for distinct heparan sulfate epitopes.