Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Type Identification from Single-Cell Transcriptomic Data via Semi-supervised Learning

Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Neural networks have been employed to identify cell types from scRNAseq data with high performance. However, it requires a large mount of individual cells with accurate and unbiased annotated types to build the identification models. Unfortunately, labeling the scRNAseq data is cumbersome and time-consuming as it involves manual inspection of marker genes. To overcome this challenge, we propose a semi-supervised learning model to use unlabeled scRNAseq cells and limited amount of labeled scRNAseq cells to implement cell identification. Firstly, we transform the scRNAseq cells to "gene sentences", which is inspired by similarities between natural language system and gene system. Then genes in these sentences are represented as gene embeddings to reduce data sparsity. With these embeddings, we implement a semi-supervised learning model based on recurrent convolutional neural networks (RCNN), which includes a shared network, a supervised network and an unsupervised network. The proposed model is evaluated on macosko2015, a large scale single-cell transcriptomic dataset with ground truth of individual cell types. It is observed that the proposed model is able to achieve encouraging performance by learning on very limited amount of labeled scRNAseq cells together with a large number of unlabeled scRNAseq cells.
Correlations of Asthma Mortality With Traffic-Related Factors: Use of Catalytic Converters and Radial Tires

Objective: The objective of this study was to test the hypotheses that the post-1970 rise in asthma mortality in industrialized nations was related to introduction of catalytic converters and/or radial tires. Methods: Annual asthma mortality data were plotted on linear coordinates for fraction of automobile fleet with converters or radial tires in Canada, Germany, Japan, and the United States. Results: Catalytic converter association could not account for asthma mortality that rose in Germany before general adoption of the technology there. Radial tire use was, however, linearly correlated with asthma mortality in all four countries. Conclusion: Rising exposure to materials related to radial tire use may account for a substantial fraction of increased asthma mortality risk since approximately 1970.
Comparative distribution of estrogen receptor‐α and ‐β mRNA in the rat central nervous system

Estrogen plays a profound role in regulating the structure and function of many neuronal systems in the adult rat brain. The actions of estrogen were thought to be mediated by a single nuclear estrogen receptor (ER) until the recent cloning of a novel ER (ER‐β). To ascertain which ER is involved in the regulation of different brain regions, the present study compared the distribution of the classical (ER‐α) and novel (ER‐β) forms of ER mRNA‐expressing neurons in the central nervous system (CNS) of the rat with in situ hybridization histochemistry. Female rat brain, spinal cord, and eyes were frozen, and cryostat sections were collected on slides, hybridized with [35S]‐labeled antisense riboprobes complimentary to ER‐α or ER‐β mRNA, stringently washed, and opposed to emulsion. The results of these studies revealed the presence of ER‐α and ER‐β mRNA throughout the rostral‐caudal extent of the brain and spinal cord. Neurons of the olfactory bulb, supraoptic, paraventricular, suprachiasmatic, and tuberal hypothalamic nuclei, zona incerta, ventral tegmental area, cerebellum (Purkinje cells), laminae III–V, VIII, and IX of the spinal cord, and pineal gland contained exclusively ER‐β mRNA. In contrast, only ER‐α hybridization signal was seen in the ventromedial hypothalamic nucleus and subfornical organ. Perikarya in other brain regions, including the bed nucleus of the stria terminalis, medial and cortical amygdaloid nuclei, preoptic area, lateral habenula, periaqueductal gray, parabrachial nucleus, locus ceruleus, nucleus of the solitary tract, spinal trigeminal nucleus and superficial laminae of the spinal cord, contained both forms of ER mRNA. Although the cerebral cortex and hippocampus contained both ER mRNAs, the hybridization signal for ER‐α mRNA was very weak compared with ER‐β mRNA. The results of these in situ hybridization studies provide detailed information about the distribution of ER‐α and ER‐β mRNAs in the rat CNS. In addition, this comparative study provides evidence that the region‐specific expression of ER‐α, ER‐β, or both may be important in determining the physiological responses of neuronal populations to estrogen action. J. Comp. Neurol. 388:507–525, 1997. © 1997 Wiley‐Liss, Inc.
Kruppel-like factor 6 (KLF6) is a tumor-suppressor gene frequently inactivated in colorectal cancer.

BACKGROUND & AIMS Kruppel-like factor 6 (KLF6) is a ubiquitous zinc finger tumor suppressor that is often mutated in prostate cancer. Our aims were to establish the frequency of KLF6 inactivation in sporadic and inflammatory bowel disease (IBD)-associated colorectal cancers (CRC); to correlate these abnormalities with mutation and/or loss of TP53, APC, and K-RAS; and to characterize the behavior of mutant KLF6 in colon-derived cell lines. METHODS We analyzed DNA isolated from 50 microdissected CRC cases, including 35 sporadic and 15 IBD-associated tumors. Microsatellite analysis and direct sequencing were used to establish the incidence of microsatellite instability, KLF6 and TP53 allelic imbalance, and KLF6, K-RAS, TP53, and APC mutation. Loss of growth suppressive function of the CRC-derived KLF6 mutants was characterized by in vitro thymidine incorporation assays and Western blotting. RESULTS KLF6 was inactivated by loss and/or mutation in most sporadic and IBD-related CRCs. The KLF6 locus was deleted in at least 55% of tumors, and mutations were identified in 44%. Rates of KLF6 loss and mutation were similar to those of TP53 and K-RAS in the same samples. KLF6 mutations were present in tumors with either microsatellite or chromosomal instability and were more common, particularly in the IBD-related cancers, in the presence of wild-type APC. Unlike wild-type KLF6, cancer-derived KLF6 mutants neither suppressed growth nor induced p21 following transfection into cultured cells. CONCLUSIONS Deregulation of KLF6 by a combination of allelic imbalance and mutation may play a role in the development of CRC.
Proteome diversification by adenosine to inosine RNA-editing

Nucleotide deamination is a widespread phenomenon frequently leading to a change of the genetic information. Adenosine deaminases that act on RNA (ADARs) convert adenosines to inosines in double-stranded or structured regions of RNAs. Inosines are interpreted as guanosines by most cellular processes and hence, this type of modification can affect the coding potential of an RNA but also its splicing, folding, or stability, to name a few. While originally believed to be a rare event recent bioinformatic screens have demonstrated that RNA-editing by ADARs is widespread and very abundant in mammals. From these screens, editing sites were discovered in both coding and non-coding regions of mRNAs. In this review we focus on RNA-editing events that alter the coding potential of mRNAs and hence lead to the formation of proteins that differ from their genomically encoded versions. We will therefore discuss the role of ADARs in proteome diversification, in particular in the nervous system where editing is most abundant.
Analytical evaluation of the signal and noise propagation in x-ray differential phase-contrast computed tomography

We analyze the signal and noise propagation of differential phase-contrast computed tomography (PCT) compared with conventional attenuation-based computed tomography (CT) from a theoretical point of view. This work focuses on grating-based differential phase-contrast imaging. A mathematical framework is derived that is able to analytically predict the relative performance of both imaging techniques in the sense of the relative contrast-to-noise ratio for the contrast of any two materials. Two fundamentally different properties of PCT compared with CT are identified. First, the noise power spectra show qualitatively different characteristics implying a resolution-dependent performance ratio. The break-even point is derived analytically as a function of system parameters such as geometry and visibility. A superior performance of PCT compared with CT can only be achieved at a sufficiently high spatial resolution. Second, due to periodicity of phase information which is non-ambiguous only in a bounded interval statistical phase wrapping can occur. This effect causes a collapse of information propagation for low signals which limits the applicability of phase-contrast imaging at low dose.
3D-printed silicate porous bioceramics using a non-sacrificial preceramic polymer binder

Silicate bioceramics possess an excellent bioactivity; however, shaping them into complex geometries is still challenging. Therefore, this paper aims to present a new strategy for the shaping of a bioglass-ceramic with controlled geometry and properties starting from a glass powder combined with a preceramic polymer, i.e. a silicon resin, and reactive fillers. The powder-based three-dimensional (3D)-printing of wollastonite (CaSiO3)-based silicate bioceramic parts was demonstrated in this work. The resin plays a dual role, as it not only acts as a non-sacrificial binder for the filler powders in the printing process but it also reacts with the fillers to generate the desired bioceramic phases. The mechanical and physical properties, i.e. ball-on-three-balls test, density, porosity and morphology, were evaluated in 3D-printed discs. These samples possessed a total porosity around 64 vol% and a biaxial flexural strength around 6 MPa. The raw materials used in this work also enabled the 3D-printing of scaffolds possessing a designed multi-scale porosity, suitable bioceramic phase assemblage and a compressive strength of 1 MPa (for cylindrical scaffolds with total porosity ∼80 vol%). Solubility in TRIS/HCl and in vitro assays, i.e. viability, cytotoxicity and apoptosis assays, were also performed. In vitro tests indicated good cell viability and no cytotoxicity effect on the cells.
Drop Impact Reliability Analysis of 3-D Chip-on-Chip Packaging: Numerical Modeling and Experimental Validation

This paper aims at investigating the drop impact solder interconnect reliability of an advanced ultra-fine-pitch 3-D integrated circuit chip stacking packaging in accordance with JEDEC board-level test specification through finite-element (FE) simulation and experimental testing. To characterize the transient dynamic responses of the package, ANSYS/LS-DYNA incorporated with the Input-G method is applied. To well simulate the mechanical behaviors of the solder interconnects, a strain-rate-dependent elastoplastic Johnson-Cook constitutive model for the Sn3.5Ag solder is applied. In addition, an inverse calculation is carried out to identify the overall structural damping of the dynamic system. Furthermore, a JEDEC-compliant drop tester is used to conduct the drop test, where failure analysis is performed using an optical microscope. Moreover, a simplified Darveaux fatigue life prediction model is constructed based on the calculated strain energy densities at different JEDEC test conditions together with the corresponding drop test data. To demonstrate the validity of the developed fatigue life prediction model, a confirmatory experiment is performed. Finally, parametric FE study incorporated with experimental design is performed to seek a design guideline for enhanced solder interconnect reliability under drop impact. Both the experimental and simulation data reveal that underfill can greatly enhance the drop impact reliability of the solder interconnects. In addition, the cornered interconnects and even package in a one-component configuration would fail earlier than the central ones, with a cohesive fracture in the Sn3.5Ag solder rather than the intermetallic compound (IMC) and its interface. Besides, an increasing IMC thickness reduces the drop impact solder interconnect reliability while enhancing the thermal cycling one.
Treatment of congenital upper extremity problems.

LEARNING OBJECTIVES After studying this article, the participant should be able to: 1. Describe the terminology and classification of congenital hand anomalies. 2. Describe the incidence and embryogenesis of some common congenital hand anomalies. 3. Discuss the general principles and goals for treatment of congenital hand anomalies. 4. Describe the management of five of the more common congenital hand anomalies (syndactyly, short digits, thumb duplication, hypoplastic thumb, and radial dysplasia). SUMMARY Congenital hand anomalies can cause substantial emotional and functional problems. This article reviews the etiology, classification, and management of some of the more common hand anomalies. A general approach to the patient and the goals of treatment are reviewed, as is the approach to five specific congenital hand anomalies: syndactyly, short digits, thumb duplication, hypoplastic thumb, and radial dysplasia.
Interspecific Competition, Environmental Gradients, Gene Flow, and the Coevolution of Species' Borders

Darwin viewed species range limits as chiefly determined by an interplay between the abiotic environment and interspecific interactions. Haldane argued that species' ranges could be set intraspecifically when gene flow from a species’ populous center overwhelms local adaptation at the periphery. Recently, Kirkpatrick and Barton have modeled Haldane’s process with a quantitative genetic model that combines density‐dependent local population growth with dispersal and gene flow across a linear environmental gradient in optimum phenotype. To address Darwin’s ideas, we have extended the Kirkpatrick and Barton model to include interspecific competition and the frequency‐dependent selection that it generates, as well as stabilizing selection on a quantitative character. Our model includes local population growth, movements over space, natural selection, and gene flow. It simultaneously addresses the evolution of character displacement and species borders. It reproduces the Kirkpatrick and Barton single‐species result that limited ranges can be produced with sufficiently steep environmental gradients and strong dispersal. Further, in the absence of environmental gradients or barriers to dispersal, interspecific competition will not limit species ranges at evolutionary equilibrium. However, interspecific competition can interact with environmental gradients and gene flow to generate limited ranges with much less extreme gradient and dispersal parameters than in the single‐species case. Species display character displacement in sympatry, yet the reduction in competition that results from this displacement does not necessarily allow the two species to become sympatric everywhere. When species meet, competition reduces population densities in the region of overlap, which, in turn, intensifies the asymmetry in gene flow from center to margin. This reduces the ability of each species to adapt to local physical conditions at their range limits. If environmental gradients are monotonic but not linear, the transition zone between species at coevolutionary equilibrium occurs where the environmental gradient is steepest. If productivity gradients are also introduced into the model, then patterns similar to Rapoport’s rule emerge. Interacting species respond to climate change, as it affects the optimal phenotype over space, by a combination of range shifts and local evolution in mean phenotype, while solitary species respond solely by range shifts. Finally, we compare empirical estimates for intrinsic growth rates and diffusion coefficients for several species to those needed by the single‐species model to produce a stable limited range. These empirical values are generally insufficient to produce limited ranges in the model suggesting a role for interspecific interactions.
Site-directed Mutagenesis of Nitrate Reductase from Aspergillus nidulans

Nitrate reductase is a multiredox enzyme possessing three functional domains associated with the prosthetic groups FAD, heme iron, and molybdopterin. In Aspergillus nidulans, it is encoded by the niaD gene. A homologous transformation system has been used whereby a major deletion at the niiAniaD locus of the host was repaired by gene replacement. Employing site-directed mutagenesis and this transformation system, nine niaD mutants were generated carrying specific amino acid substitutions. Mutants in which alanine replaced cysteine 150, which is thought to bind the molybdenum atom of the molybdenum-pterin, and in which alanine replaced histidine 547, which putatively binds heme iron, had no detectable nitrate reductase (NAR) activity. This clearly establishes an essential catalytic role for these residues. Of the remaining mutants, all altered in the NADPH/FAD domain, two were temperature-sensitive for NAR activity, two had reduced NAR activity levels, and three had normal levels. Since some of these mutants change residues conserved between homologous nitrate reductases from a wide range of species, it is clear that such amino acid identities do not necessarily signify essential roles for the activity of the enzyme. These findings are considered in the light of predicted structural/functional roles for the altered amino acids.
Diversity and Seasonality of Bioluminescent Vibrio cholerae Populations in Chesapeake Bay

ABSTRACT Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species.
Evidence-Based Medicine Evidence-Based Medicine , Systematic Reviews , and Guidelines in Interventional Pain Management : Part 4 : Observational Studies

search and describes it as a shift in medical paradigms, in contrast to intuition, unsystematic clinical experience, and pathophysiologic rationale. While the importance of randomized trials has been created by the concept of the hierarchy of evidence in guiding therapy, much of the medical research is observational. There is competition, contrast, and a feeling of inferiority and uselessness for observational studies, created by a lack of understanding of medical research. However, observational studies and randomized clinical trials (RCTs) can be viewed as the steps of observation and experimentation that form the basis of the scientific methodology. Further, rational healthcare practices require knowledge about the etiology and pathogenesis, diagnosis, prognosis, and treatment of disorders.
Comparison between eight‐ and sixteen‐channel TEM transceive arrays for body imaging at 7 T

Eight‐ and sixteen‐channel transceive stripline/TEM body arrays were compared at 7 T (297 MHz) both in simulation and experiment. Despite previous demonstrations of similar arrays for use in body applications, a quantitative comparison of the two configurations has not been undertaken to date. Results were obtained on a male pelvis for assessing transmit, signal to noise ratio, and parallel imaging performance and to evaluate local power deposition versus transmit B1 (B1+). All measurements and simulations were conducted after performing local B1+ phase shimming in the region of the prostate. Despite the additional challenges of decoupling immediately adjacent coils, the sixteen‐channel array demonstrated improved or nearly equivalent performance to the eight‐channel array based on the evaluation criteria. Experimentally, transmit performance and signal to noise ratio were 22% higher for the sixteen‐channel array while significantly increased reduction factors were achievable in the left–right direction for parallel imaging. Finite difference time domain simulations demonstrated similar results with respect to transmit and parallel imaging performance, however, a higher transmit efficiency advantage of 33% was predicted. Simulations at both 3 and 7 T verified the expected parallel imaging improvements with increasing field strength and showed that, for a specific B1+ shimming strategy used, the sixteen‐channel array exhibited lower local and global specific absorption rate for a given B1+. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
Acute effect of whey peptides upon blood pressure of hypertensive rats, and relationship with their angiotensin-converting enzyme inhibitory activity.

SCOPE The aim of this study was to investigate the antihypertensive effect of a peptide fraction (PepC) obtained from a whey protein concentrate following hydrolysis by Cynara cardunculus, as well as of its fraction with MW below 3 kDa (PepCF). Both these concentrates encompassed peptides that exhibited potent in vitro inhibition of angiotensin-converting enzyme (ACE): two were released from α-lactalbumin--KGYGGVSLPEW and DKVGINYW, and one from β-lactoglobulin--DAQSAPLRVY. METHODS AND RESULTS Upon oral administration, by gastric intubation, of 400 mg/kg body weight (bw) of those peptide concentrates, or 5 mg/kg bw of the corresponding synthetic peptides, to 12 wk-old spontaneously hypertensive rats (SHR), the systolic and diastolic blood pressures were monitored by the tail-cuff method--before, and 2, 4, 6, 8 and 24 h afterwards. Water and zofenopril (5 mg/kg bw)--a known ACE-inhibitor, were used as negative and positive controls, respectively. Acute administration of PepC, PepCF, KGYGGVSLPEW, DKVGINYW and DAQSAPLRVY caused antihypertensive effects in SHR; the maximum effect occurred by 4 h and 6 h after administration of the peptide concentrates and the synthetic peptides, respectively. PepC and KGYGGVSLPEW also showed ACE-inhibitory activity in vivo: the pressor effect of angiotensin I was significantly lower, and the response to bradykinin increased when the rats were pre-treated with either product. CONCLUSION Our results strongly suggest that PepC will be effective as nutraceutical ingredient for the formulation of functional foods aimed at hypertension control.