Miracle-dz/UniFAR-FTUs huggingface dataset:
Fabrication of multilayer microstructures using dry film resist and deep reactive ion etcher

In this Letter, the authors demonstrate fabrication of multilevel microstructures using inductively coupled plasma deep reactive ion etcher (ICP-DRIE) in conjunction with dry film photoresist (DFR) as etch mask. By limiting the usage of photoresist on the layers, both the chances of introducing contamination as well as wastage of photoresist are reduced. Thus, combining DFR with DRIE in microfabricating of multilevel microstructure has the potential to significantly reduce fabrication time, cost and contamination.
The impact of cosmic variance on simulating weak lensing surveys

Upcoming weak lensing surveys will survey large cosmological volumes to measure the growth of cosmological structure with time and thereby constrain dark energy. One major systematic uncertainty in this process is the calibration of the weak lensing shape distortions, or shears. Most upcoming surveys plan to test several aspects of their shear estimation algorithms using sophisticated image simulations that include realistic galaxy populations based on high-resolution data from the Hubble Space Telescope (HST). However, existing datasets from the HST cover very small cosmological volumes, so cosmic variance could cause the galaxy populations in them to be atypical. A narrow redshift slice from such surveys could be dominated by a single large overdensity or underdensity. In that case, the morphology-density relation could alter the local galaxy populations and yield an incorrect calibration of shear estimates as a function of redshift. We directly test this scenario using the COSMOS survey, the largest-area HST survey to date, and show how the statistical distribu"
Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies

Analysis of epigenetic mechanisms, particularly DNA methylation, is of increasing interest for epidemiologic studies examining disease etiology and impacts of environmental exposures. The Infinium HumanMethylation450 BeadChip® (450K), which interrogates over 480 000 CpG sites and is relatively cost effective, has become a popular tool to characterize the DNA methylome. For large-scale studies, minimizing technical variability and potential bias is paramount. The goal of this paper was to evaluate the performance of several existing and novel color channel normalizations designed to reduce technical variability and batch effects in 450K analysis from a large population study. Comparative assessment of 10 normalization procedures included the GenomeStudio® Illumina procedure, the lumi smooth quantile approach, and the newly proposed All Sample Mean Normalization (ASMN). We also examined the performance of normalizations in combination with correction for the two types of Infinium chemistry utilized on the 450K array. We observed that the performance of the GenomeStudio® normalization procedure was highly variable and dependent on the quality of the first sample analyzed in an experiment, which is used as a reference in this procedure. While the lumi normalization was able to decrease batch variability, it increased variation among technical replicates, potentially reducing biologically meaningful findings. The proposed ASMN procedure performed consistently well, both at reducing batch effects and improving replicate comparability. In summary, the ASMN procedure can improve existing color channel normalization, especially for large epidemiologic studies, and can be successfully implemented to enhance a 450K DNA methylation data pipeline.
Notch Signaling Promotes Growth and Invasion in Uveal Melanoma

Purpose: To determine whether uveal melanoma, the most common primary intraocular malignancy in adults, requires Notch activity for growth and metastasis. Experimental Design: Expression of Notch pathway members was characterized in primary tumor samples and in cell lines, along with the effects of Notch inhibition or activation on tumor growth and invasion. Results: Notch receptors, ligands, and targets were expressed in all five cell lines examined and in 30 primary uveal melanoma samples. Interestingly, the three lines with high levels of baseline pathway activity (OCM1, OCM3, and OCM8) had their growth reduced by pharmacologic Notch blockade using the γ-secretase inhibitor (GSI) MRK003. In contrast, two uveal melanoma lines (Mel285 and Mel290) with very low expression of Notch targets were insensitive to the GSI. Constitutively active forms of Notch1 and Notch2 promoted growth of uveal melanoma cultures and were able to rescue the inhibitory effects of GSI. MRK003 treatment also inhibited anchorage-independent clonogenic growth and cell invasion and reduced phosphorylation levels of STAT3 and extracellular signal-regulated kinase (Erk)1/2. Suppression of canonical Notch activity using short hairpin RNA targeting Notch2 or CBF1 was also able to reduce tumor growth and invasion. Finally, intraocular xenograft growth was significantly decreased by GSI treatment. Conclusion: Our findings suggest that Notch plays an important role in inducing proliferation and invasion in uveal melanoma and that inhibiting this pathway may be effective in preventing tumor growth and metastasis. Clin Cancer Res; 18(3); 654–65. ©2012 AACR.
DEVELOPMENT OF DESIGN CRITERIA FOR REINFORCED CONCRETE BOX CULVERTS. PART I: STRENGTH AND BEHAVIOR OF REINFORCED CONCRETE BEAMS AND FRAMES.

Abstract : The results of 57 tests on simply-supported beams and 24 tests on frame members are described and correlated in this report. The main object of these tests was to study the behavior and strength in shear of reinforced concrete members; a few tests were intended to study the flexural strength of under-reinforced members under axial load and bending. The ultimate objective of the test program was to obtain information which would permit the development of more rational design criteria for reinforced concrete box culverts. Fundamental knowledge was first acquired through tests of simplysupported beams under various conditions of loading. And, finally, tests were made on 24 frames under conditions simulating closely those in the horizontal member of a box culvert section; three of these frames had web reinfrocement in the form of bent bars. The following major variables were studied during the course of the investigation: type of loading, concrete strength, steel percentage, ratio of span length to effective depth, ratio of shear span to effective depth, and ratio of axial to vertical load. The simply-supported beams were tested under one or two concentrated loads, or under uniform load.
Optimal Feature Extraction and Classification of Tensors via Matrix Product State Decomposition

Big data consists of large multidimensional datasets that would often be difficult to analyze if working with the original tensor. There is a rising interest in the use of tensor decompositions for feature extraction due to the ability to extract necessary features from a large dimensional feature space. In this paper the matrix product state (MPS) decomposition is used for feature extraction of large tensors. The novelty of the paper is the introduction of a single core tensor obtained from the MPS that not only contains a significantly reduced feature space, but can perform classification with high accuracy without the need of feature selection methods.
Reading and Thinking: Re-read LSTM Unit for Textual Entailment Recognition

Recognizing Textual Entailment (RTE) is a fundamentally important task in natural language processing that has many applications. The recently released Stanford Natural Language Inference (SNLI) corpus has made it possible to develop and evaluate deep neural network methods for the RTE task. Previous neural network based methods usually try to encode the two sentences (premise and hypothesis) and send them together into a multi-layer perceptron to get their entailment type, or use LSTM-RNN to link two sentences together while using attention mechanic to enhance the model’s ability. In this paper, we propose to use the re-read mechanic, which means to read the premise again and again while reading the hypothesis. After read the premise again, the model can get a better understanding of the premise, which can also affect the understanding of the hypothesis. On the contrary, a better understanding of the hypothesis can also affect the understanding of the premise. With the alternative re-read process, the model can “think” of a better decision of entailment type. We designed a new LSTM unit called re-read LSTM (rLSTM) to implement this “thinking” process. Experiments show that we achieve results better than current state-of-the-art equivalents.
Characterization of herpes simplex virus type 1 L-particle assembly and egress in hippocampal neurones by electron cryo-tomography

Visualizing virus–host interactions in situ inside infected cells by electron cryo‐tomography provides unperturbed snapshots of the infection process. Here we focus on the assembly and egress pathway of herpesviruses. Cells infected with herpes simplex virus 1 produce and release not only infective virions but also non‐infectious light particles (L‐particles). L‐particles are devoid of viral capsids and genomes. In this study, we analysed L‐particle assembly and egress pathways in cultured dissociated hippocampus neurones by electron cryo‐tomography. Virion and L‐particle formation occurred in close proximity, suggesting shared assembly and exit pathways. Clathrin‐like coats were occasionally associated with L‐particle and virion assembly sites. Further, we compared the three‐dimensional ultrastructure of intracellular and extracellular L‐particles and quantified their diameters and the abundance of inclusion bodies contained.
Machine or Human? Evaluating the Quality of a Language Translation Mobile App for Diabetes Education Material

Background Diabetes is a major health crisis for Hispanics and Asian Americans. Moreover, Spanish and Chinese speakers are more likely to have limited English proficiency in the United States. One potential tool for facilitating language communication between diabetes patients and health care providers is technology, specifically mobile phones. Objective Previous studies have assessed machine translation quality using only writing inputs. To bridge such a research gap, we conducted a pilot study to evaluate the quality of a mobile language translation app (iTranslate) with a voice recognition feature for translating diabetes patient education material. Methods The pamphlet, “You are the heart of your family…take care of it,” is a health education sheet for diabetes patients that outlines three recommended questions for patients to ask their clinicians. Two professional translators translated the original English sentences into Spanish and Chinese. We recruited six certified medical translators (three Spanish and three Chinese) to conduct blinded evaluations of the following versions: (1) sentences interpreted by iTranslate, and (2) sentences interpreted by the professional human translators. Evaluators rated the sentences (ranging from 1-5) on four scales: Fluency, Adequacy, Meaning, and Severity. We performed descriptive analyses to examine the differences between these two versions. Results Cronbach alpha values exhibited high degrees of agreement on the rating outcomes of both evaluator groups: . 920 for the Spanish raters and . 971 for the Chinese raters. The readability scores generated using MS Word’s Flesch-Kincaid Grade Level for these sentences were 0.0, 1.0, and 7.1. We found iTranslate generally provided translation accuracy comparable to human translators on simple sentences. However, iTranslate made more errors when translating difficult sentences. Conclusions Although the evidence from our study supports iTranslate’s potential for supplementing professional human translators, further evidence is needed. For this reason, mobile language translation apps should be used with caution.
Automatic clustering of orthologs and inparalogs shared by multiple proteomes

MOTIVATION The complete sequencing of many genomes has made it possible to identify orthologous genes descending from a common ancestor. However, reconstruction of evolutionary history over long time periods faces many challenges due to gene duplications and losses. Identification of orthologous groups shared by multiple proteomes therefore becomes a clustering problem in which an optimal compromise between conflicting evidences needs to be found. RESULTS Here we present a new proteome-scale analysis program called MultiParanoid that can automatically find orthology relationships between proteins in multiple proteomes. The software is an extension of the InParanoid program that identifies orthologs and inparalogs in pairwise proteome comparisons. MultiParanoid applies a clustering algorithm to merge multiple pairwise ortholog groups from InParanoid into multi-species ortholog groups. To avoid outparalogs in the same cluster, MultiParanoid only combines species that share the same last ancestor. To validate the clustering technique, we compared the results to a reference set obtained by manual phylogenetic analysis. We further compared the results to ortholog groups in KOGs and OrthoMCL, which revealed that MultiParanoid produces substantially fewer outparalogs than these resources. AVAILABILITY MultiParanoid is a freely available standalone program that enables efficient orthology analysis much needed in the post-genomic era. A web-based service providing access to the original datasets, the resulting groups of orthologs, and the source code of the program can be found at http://multiparanoid.cgb. ki.se.
Impact of Glomerular Kidney Diseases on the Clearance of Drugs

Numerous physiologic variations, including urinary protein excretion, low serum albumin concentrations, and reductions in kidney function (clearance), exist in patients with glomerulonephritis. These factors could alter the disposition of numerous drugs. The purpose of the current article was to review the influence of glomerulonephritis on the pharmacokinetics of drugs used clinically or experimentally in the treatment of these conditions. Several articles or presentations were located that reported on the pharmacokinetics of immunosuppressant, cytotoxic, and therapeutic antibody drugs in populations with glomerulonephritis. Most publications reported an increase in systemic clearance in glomerulonephritis as compared with populations in whom the drugs were typically used and in patients with nonglomerular forms of chronic kidney disease. It appears that the increase in systemic clearance is predominantly through nonrenal clearance pathways, although enhancement of renal clearance has also been appreciated for some drugs. Available preliminary data suggest specific alterations in the activity of individual pathways of drug metabolism and transport. Recommendations are provided for the design of future studies of drugs in the glomerulonephritis population and for inclusion of patients with urinary protein excretion in studies that assess drug pharmacokinetics.
Tight Bounds on the Complexity of Parallel Sorting

In this paper, we prove tight upper and lower bounds on the number of processors, information transfer, wire area, and time needed to sort N numbers in a bounded-degree fixed-connection network. Our most important new results are: 1) the construction of an N-node degree-3 network capable of sorting N numbers in O(log N) word steps; 2) a proof that any network capable of sorting N (7 log N)-bit numbers in T bit steps requires area A where AT2 = ¿(N2 log2 N); and 3) the construction of a ``small-constant-factor'' bounded-degree network that sorts N ¿(log N)-bit numbers in T = ¿(log N) bit steps with A = ¿(N2) area.
Simulation of Multiple Hydraulic Fracturing in Non-Uniform Pore Pressure Field

A series of numerical simulations of hydraulic fracturing were performed to study the initiation, propagation and breakdown of fluid driven fractures. The simulations are conducted with a flow-coupled Rock Failure Process Analysis code (RFPA2D). Both heterogeneity and permeability of the rocks are taken into account in the studies. The simulated results reflect macroscopic failure evolution process induced by microscopic fracture subjected to porosity pressure, which are well agreeable to the character of multiple hydraulic fracturing experiments. Based on the modeling results, it is pointed out that fracture is influenced not only by pore pressure magnitude on a local scale around the fracture tip but also by the orientation and the distribution of pore pressure gradients on a global scale. The fracture initiation, the orientation of crack path, the breakdown pressure and the stress field evolution around the fracture tip are influenced considerably by the orientation of the pore pressure. The research provides valuable guidance to the designers of hydraulic fracturing engineering.
Automatic acquired domain knowledge for ad hoc search: evaluated results

The automatic acquisition of usable domain knowledge is a challenging issue. Such knowledge can be employed to assist a user in searching a document collection. This can be done by suggesting query modification options based on the knowledge uncovered by analyzing the document collection. We acquire such knowledge by simply exploiting the documents' markup structure. This gives us a domain model tailored to the particular collection. But how good is such a model? We present results of two evaluations. The first one looks at the actual domain model. We will discuss how users judged the relations encoded in the model. The second evaluation is task-based and goes a step further. It investigates how a search system that applies the automatically constructed domain model performs compared to a standard search system.
Cell-Specific Regulation of Nucleic Acid Sensor Cascades: a Controlling Interest in the Antiviral Response

ABSTRACT In this study, we examined the capacities of non-antigen-presenting cell types to propagate antiviral signals following infection with recombinant adenovirus or by direct nucleic acid transfection. Three murine cell lines (RAW264.7 macrophages as a positive control, FL83B hepatocytes, and MS1 endothelial cells) were assessed following exposure to adenovirus, DNA, or RNA ligands. Based on primary (interferon response factor 3 [IRF3] phosphorylation) and secondary (STAT1/2 phosphorylation) response markers, we found each cell line presented a unique response profile: RAW cells were highly responsive, MS1 cells were modified in their response, and FL83B cells were essentially nonresponsive. Comparative reverse transcription-quantitative PCR (RT-qPCR) of nucleic acid sensing components revealed major differences between the three cell types. A prominent difference was at the level of adaptor molecules; TRIF, MyD88, MAVS, and STING. TRIF was absent in MS1 and FL83B cells, whereas MyD88 levels were diminished in FL83B hepatocytes. These differences resulted in compromised TLR-mediated activation. While the cytosolic adaptor MAVS was well represented in all cell lines, the DNA adaptor STING was deficient in FL83B hepatocytes (down by nearly 3 log units). The absence of STING provides an explanation for the lack of DNA responsiveness in these cells. This hypothesis was confirmed by acquisition of IRF3 activation in Flag-STING FL83B cells following DNA transfection. To consolidate the central role of adaptors in MS1 endothelial cells, short hairpin RNA (shRNA) knockdown of STING and MAVS resulted in a ligand-specific loss of IRF3 responsiveness. In contrast to the requirement for specific adaptor proteins, a requirement for a specific DNA sensor (AIM2, DDx41, or p204) in the IRF3 activation response was not detected by shRNA knockdown in MS1 cells. The data reveal that cell-specific regulation of nucleic acid sensing cascade components influences antiviral recognition responses, that controlling levels of adaptor molecules is a recurring strategy in regulating antiviral recognition response functions, and that comparative RT-qPCR has predictive value for antiviral/innate response functions in these cells.
Inflammation in cardiac injury, repair and regeneration

Purpose of review Cardiomyocyte necrosis activates an inflammatory response that serves to clear the injured myocardium from dead cells, and stimulates repair, but may also extend injury. This manuscript discusses new findings that advanced our understanding of the role of inflammation in cardiac injury and repair. Recent findings Recently published studies have identified interleukin-1&agr; and RNA released by necrotic cardiomyocytes as key danger signals that trigger the inflammatory response following infarction. Interleukin-1 promotes activation of a proinflammatory phenotype in leukocytes and fibroblasts, and delays myofibroblast transdifferentiation. Inhibitory lymphocytes play a crucial role in negative regulation of the postinfarction inflammatory response by modulating macrophage and fibroblast phenotype. Cardiac macrophages exhibit significant heterogeneity and phenotypic plasticity and may orchestrate the reparative response following infarction. In neonatal mice, resident embryonic macrophage subpopulations may promote a regenerative response. In contrast, in adult animals replacement of resident macrophage populations with monocyte-derived macrophages may induce inflammation while inhibiting cardiac regeneration. These exciting observations highlight the crucial role of macrophages in cardiac injury and repair, but should be interpreted with caution considering the limitations of murine models of neonatal myocardial injury. Summary Design of novel strategies to reduce cardiac injury, improve repair and promote regeneration is dependent on understanding of the cell biology of the inflammatory response.
Team Diversity and Performance - How Agile Practices and Psychological Safety Interact

Information system development is largely dependent on social interaction and team work. Team composition, team processes, and behavior among, as well as agile practices used by team members play an important role for the success of information system development projects. Especially team resilience, the capacity to recover quickly from crises, is important in an ever-changing environment. Recent research in organizational psychology found team diversity and psychological safety to be important factors for team performance. In increasing diverse teams, these findings become more and more important. In this paper, we propose a model and research design to investigate the effects of team diversity, psychological safety, and social agile practices on team resilience and team performance in agile software development. The proposed model combines recent research in the field of organizational psychology with agile information system research to provide a better understanding of the team-level effects at play in agile software development.
นิพนธ์ต้นฉบับ Is anesthetic gel necessary in outpatient flexible cystoscopy ?

Objectives To study the benefit of intraurethral lidocaine jelly instillation before flexible cystoscopic examination regarding patients tolerance to pain compared with the plain lubricant. Research design Randomized prospective study Setting The Outpatient Urologic Clinic at King Chulalongkorn Memorial Hospital Methods We compared the anesthetic effect of 10 cc intraurethral 2 % lidocaine jelly (N= 80) and 10 cc plain lubricant (N = 80) for outpatient flexible cystoscope in male patients. The age, diagnosis, prostatic size and examination time were recorded. After the procedure, the following data of the patient were recorded: level of pain experienced during gel instillation, during cystoscopic examination based on a 100 mm. visual analog scale. A questionnaire on satisfaction of anesthesia, requirement of analgesic drug, willingness to use the same anesthesia for next cystoscopy and requirement of general or spinal anesthesia for next cystoscopy were also recoreded. นิพนธ์ต้นฉบับ