Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Cell Detection in Bright-Field Microscope Images Using SIFT, Random Forests, and Hierarchical Clustering

We present a novel machine learning-based system for unstained cell detection in bright-field microscope images. The system is fully automatic since it requires no manual parameter tuning. It is also highly invariant with respect to illumination conditions and to the size and orientation of cells. Images from two adherent cell lines and one suspension cell line were used in the evaluation for a total number of more than 3500 cells. Besides real images, simulated images were also used in the evaluation. The detection error was between approximately zero and 15.5% which is a significantly superior performance compared to baseline approaches.
Leveraging Transliterations from Multiple Languages

While past research on machine transliteration has focused on a single transliteration task, there exist a variety of supplemental transliterations available in other languages. Given an input for English-toHindi transliteration, for example, transliterations from other languages such as Japanese or Hebrew may be helpful in the transliteration process. In this paper, we propose the application of such supplemental transliterations to English-to-Hindi machinetransliterationviaanSVMre-ranking method with features based on n-gram alignments as well as system and alignment scores. This method achieves a relative improvement of over 10% over the base system used on its own. We further apply this method to system combination, demonstrating just under 5% relative improvement.
Bayes Error Rate Estimation Using Classifier Ensembles

The Bayes error rate gives a statistical lower bound on the error achievable for a given classification problem and the associated choice of features. By reliably estimating this rate, one can assess the usefulness of the feature set that is being used for classification. Moreover, by comparing the accuracy achieved by a given classifier with the Bayes rate, one can quantify how effective that classifier is. Classical approaches for estimating or finding bounds for the Bayes error, in general, yield rather weak results for small sample sizes; unless the problem has some simple characteristics, such as Gaussian class-conditional likelihoods. This article shows how the outputs of a classifier ensemble can be used to provide reliable and easily obtainable estimates of the Bayes error with negligible extra computation. Three methods of varying sophistication are described. First, we present a framework that estimates the Bayes error when multiple classifiers, each providing an estimate of the a posteriori class probabilities, are combined through averaging. Second, we bolster this approach by adding an information theoretic measure of output correlation to the estimate. Finally, we discuss a more general method that just looks at the class labels indicated by ensemble members and provides error estimates based on the disagreements among classifiers. The methods are illustrated for artificial data, a difficult four-class problem involving underwater acoustic data, and two problems from the Proben1 benchmarks. For data sets with known Bayes error, the combiner-based methods introduced in this article outperform existing methods. The estimates obtained by the proposed methods also seem quite reliable for the real-life data sets for which the true Bayes rates are unknown.
A Novel Recurrent Neural Network for Solving Nonlinear Optimization Problems With Inequality Constraints

This paper presents a novel recurrent neural network for solving nonlinear optimization problems with inequality constraints. Under the condition that the Hessian matrix of the associated Lagrangian function is positive semidefinite, it is shown that the proposed neural network is stable at a Karush-Kuhn-Tucker point in the sense of Lyapunov and its output trajectory is globally convergent to a minimum solution. Compared with variety of the existing projection neural networks, including their extensions and modification, for solving such nonlinearly constrained optimization problems, it is shown that the proposed neural network can solve constrained convex optimization problems and a class of constrained nonconvex optimization problems and there is no restriction on the initial point. Simulation results show the effectiveness of the proposed neural network in solving nonlinearly constrained optimization problems.
Caveolin-1 Deficiency Increases Cerebral Ischemic Injury

Caveolins (Cav), the principal structural proteins of the caveolar domains, have been implicated in the pathogenesis of ischemic injury. Indeed, changes in caveolin expression and localization have been reported in renal and myocardial ischemia. Genetic ablation of the Cav-1 gene in mice was further shown to increase the extent of ischemic injury in a model of hindlimb ischemia. However, the role of Cav-1 in the pathogenesis of cerebral ischemia remains unknown. Immunoblot and immunofluorescence analyses of rat brains subjected to middle cerebral artery occlusion revealed marked increases in endothelial Cav-1 and Cav-2 protein levels. To directly assess the functional role of caveolins in the pathogenesis of cerebral ischemic injury, we next investigated the effects of cerebral ischemia in caveolin knockout (KO) mice. Interestingly, Cav-1 KO mice showed a marked increase of cerebral volume of infarction, as compared with wild-type and Cav-2 KO mice. Immunofluorescence analyses showed an increased number of proliferating endothelial cells in wild-type ischemic brains, as compared with Cav-1 KO ischemic brains. Immunoblot analyses of wild-type ischemic brains showed an increase in endothelial nitric oxide synthase protein levels. Conversely, the protein levels of endothelial nitric oxide synthase remained unchanged in Cav-1 KO ischemic brains. TUNEL analysis also showed increased apoptotic cell death in Cav-1 KO ischemic brains, as compared with wild-type ischemic brains. Our findings indicate cerebral ischemia induces a marked increase in endothelial Cav-1 and Cav-2 protein levels. Importantly, genetic ablation of the Cav-1 gene in mice results in increased cerebral volume of infarction. Mechanistically, Cav-1 KO ischemic brains showed impaired angiogenesis and increased apoptotic cell death.
LT-RTPG: a new test-per-scan BIST TPG for low switching activity

A new built-in self-test (BIST) test pattern generator (TPG) design, called low-transition random TPG (LT-RTPG), is presented. An LT-RTPG is composed of a linear feedback shift register (LFSR), a /spl kappa/-input AND gate, and a T flip-flop. When used to generate test patterns for test-per-scan BIST, it decreases the number of transitions that occur during scan shifting and, hence, decreases switching activity during testing. Various properties of LT-RTPGs are identified and a methodology for their design is presented. Experimental results demonstrate that LT-RTPGs designed using the proposed methodology decrease switching activity during BIST by significant amounts while providing high fault coverage.
Perceived Maternal Neglect and Adjustment Problems of High School Students

The present study was designed to examine the influence of perception of maternal neglect on emotional, social, and educational adjustment employing a quasi experimental design. From among a total of 94 students studying in grades VIII, IX, and X, top and bottom 25 students were selected on the basis of their scores on the ParentChild Relationship Scale (Nalini Rao, 1989). The former group of students constituted the high maternal neglect group, while the latter comprised the low maternal neglect group. Both the groups of students were administered the Adjustment Inventory for School Children developed by Sinha and Singh. Data were analyzed with the help of independent group t test. Results revealed significant differences in none of the three areas of adjustment implying that the students who perceive themselves to be neglected by their mothers are comparable to those who do not. The results have been discussed in terms of contextual effect and the compensatory nature of the care given by the father and other members of the family.
Can Developmental Disorders Reveal the Component Parts of the Human Language Faculty?

Differential profiles of language impairments in genetic developmental disorders have been argued to reveal the component parts of the language system and perhaps even the genetic specification of those components. Focusing predominantly on a comparison between Williams syndrome and Specific Language Impairment, we argue that the detailed level of behavioral fractionations observed in these disorders goes beyond the possible contribution of genes and implicates the developmental process as a key contributor to the cognitive outcome. Processes of compensation and interaction across development make highly specific developmental deficits unlikely; in line with this view, the actual level of specificity remains controversial, even in Specific Language Impairment (a paradigmatic example of a supposedly selective deficit). We consider the challenge of characterizing the atypical developmental process from the perspectives of brain development, cognitive development, and computational modeling. Failure to take up this challenge leaves many current explanations of developmental deficits ill-specified at best and implausible at worst.
Chromosome X-Wide Association Study Identifies Loci for Fasting Insulin and Height and Evidence for Incomplete Dosage Compensation

The X chromosome (chrX) represents one potential source for the “missing heritability” for complex phenotypes, which thus far has remained underanalyzed in genome-wide association studies (GWAS). Here we demonstrate the benefits of including chrX in GWAS by assessing the contribution of 404,862 chrX SNPs to levels of twelve commonly studied cardiometabolic and anthropometric traits in 19,697 Finnish and Swedish individuals with replication data on 5,032 additional Finns. By using a linear mixed model, we estimate that on average 2.6% of the additive genetic variance in these twelve traits is attributable to chrX, this being in proportion to the number of SNPs in the chromosome. In a chrX-wide association analysis, we identify three novel loci: two for height (rs182838724 near FGF16/ATRX/MAGT1, joint P-value = 2.71×10−9, and rs1751138 near ITM2A, P-value = 3.03×10−10) and one for fasting insulin (rs139163435 in Xq23, P-value = 5.18×10−9). Further, we find that effect sizes for variants near ITM2A, a gene implicated in cartilage development, show evidence for a lack of dosage compensation. This observation is further supported by a sex-difference in ITM2A expression in whole blood (P-value = 0.00251), and is also in agreement with a previous report showing ITM2A escapes from X chromosome inactivation (XCI) in the majority of women. Hence, our results show one of the first links between phenotypic variation in a population sample and an XCI-escaping locus and pinpoint ITM2A as a potential contributor to the sexual dimorphism in height. In conclusion, our study provides a clear motivation for including chrX in large-scale genetic studies of complex diseases and traits.
Anti-Her-2/neu antibody induces apoptosis in Her-2/neu overexpressing breast cancer cells independently from p53 status

Anti-Her-2/neu antibody is known to induce apoptosis in HER-2/neu overexpressing breast cancer cells. However, exact regulatory mechanisms mediating and controlling this phenomenon are still unknown. In the present study, we have investigated the effect of anti-Her-2/neu antibody on apoptosis of HER-2/neu overexpressing human breast cancer cell lines SK-BR-3, HTB-24, HTB-25, HTB-27, HTB-128, HTB-130 and HTB-131 in relation to p53 genotype and bcl-2 status. SK-BR-3, HTB-24, HTB-128 and HTB-130 cells exhibited mutant p53, whereas wild type p53 was found in HTB-25, HTB-27 and HTB-131 cells. All seven cell lines weakly expressed bcl-2 protein (10–20%). Anti-Her-2/neu antibody, irrespective of p53 and bcl-2 status, induced apoptosis in all 7 cell lines dose- and time-dependently and correlated with Her-2/neu overexpression. In addition, incubation of cell lines with anti-Her-2/neu antibody did not alter p53 or bcl-2 expression. Anti-HER-2/neu antibody did not induce apoptosis in HER-2/neu negative HBL-100 and HTB-132 cell lines. Our results indicate that within the panel of tested breast cancer cell lines, anti-Her-2/neu antibody-induced apoptosis was independent from the presence of intact p53. © 2001 Cancer Research Campaign http://www.bjcancer. com
Use of altered-specificity binding Oct-4 suggests an absence of pluripotent cell-specific cofactor usage

Oct-4 is a POU domain transcription factor that is critical for maintaining pluripotency and for stem cell renewal. Previous studies suggest that transcription regulation by Oct-4 at particular enhancers requires the input of a postulated E1A-like cofactor that is specific to pluripotent cells. However, such studies have been limited to the use of enhancer elements that bind other POU-protein family members in addition to Oct-4, thus preventing a ‘clean’ assessment of any Oct-4:cofactor relationships. Other attempts to study Oct-4 functionality in a more ‘stand-alone’ situation target Oct-4 transactivation domains to DNA using heterologous binding domains, a methodology which is known to generate artificial data. To circumvent these issues, an altered-specificity binding Oct-4 (Oct-4RR) and accompanying binding site, which binds Oct-4RR only, were generated. This strategy has previously been shown to maintain Oct-1:cofactor interactions that are highly binding-site and protein/binding conformation specific. This system therefore allows a stand-alone study of Oct-4 function in pluripotent versus differentiated cells, without interference from endogenous POU factors and with minimal deviation from bound wild-type protein characteristics. Subsequently, it was demonstrated that Oct-4RR and the highly transactive regions of its N-terminus determined here, and its C-terminus, have the same transactivation profile in pluripotent and differentiated cells, thus providing strong evidence against the existence of such a pluripotent cell-specific Oct-4 cofactor.
Application of Information - Theoretic Concepts in Chemoinformatics

The use of computational methodologies for chemical database mining and molecular similarity searching or structure-activity relationship analysis has become an integral part of modern chemical and pharmaceutical research. These types of computational studies fall into the chemoinformatics spectrum and usually have large-scale character. Concepts from information theory such as Shannon entropy and Kullback-Leibler divergence have also been adopted for chemoinformatics applications. In this review, we introduce these concepts, describe their adaptations, and discuss exemplary applications of information theory to a variety of relevant problems. These include, among others, chemical feature (or descriptor) selection, database profiling, and compound recall rate predictions.
Why Can Some Advanced Ethernet NICs Cause Packet Reordering?

The Intel Ethernet Flow Director is an advanced network interface card (NIC) technology. It provides the benefits of parallel receive processing in multiprocessing environments and can automatically steer incoming network data to the same core on which its application process resides. However, our analysis and experiments show that Flow Director can cause packet reordering in multiprocessing environments. In this paper, we use a simplified model to analyze why Flow Director can cause packet reordering. Our experiments verify our analysis.
Scalable Passaging of Adherent Human Pluripotent Stem Cells

Current laboratory methods used to passage adherent human pluripotent stem cells (hPSCs) are labor intensive, result in reduced cell viability and are incompatible with larger scale production necessary for many clinical applications. To meet the current demand for hPSCs, we have developed a new non-enzymatic passaging method using sodium citrate. Sodium citrate, formulated as a hypertonic solution, gently and efficiently detaches adherent cultures of hPSCs as small multicellular aggregates with minimal manual intervention. These multicellular aggregates are easily and reproducibly recovered in calcium-containing medium, retain a high post-detachment cell viability of 97%±1% and readily attach to fresh substrates. Together, this significantly reduces the time required to expand hPSCs as high quality adherent cultures. Cells subcultured for 25 passages using this novel sodium citrate passaging solution exhibit characteristic hPSC morphology, high levels (>80%) of pluripotency markers OCT4, SSEA-4, TRA-1-60 andTRA-1-81, a normal G-banded karyotype and the ability to differentiate into cells representing all three germ layers, both in vivo and in vitro.
Atypical effective connectivity of thalamo‐cortical circuits in autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopment disorder characterized by atypical connectivity within and across multiple brain systems. We aimed to explore information transmission from the sensory periphery to information processing centers of the brain across thalamo‐cortical circuits in ASD. A large multicenter dataset from the autism brain imaging data exchange was utilized. A thalamus template derived from the Automatic Anatomic Labeling atlas was subdivided into six subregions corresponding to six cortical regions using a “winner‐takes‐all” strategy. Granger causality analysis (GCA) was then applied to calculate effective connectivity from subregions of the thalamus to the corresponding cortical regions. Results demonstrate reduced effective connectivity from the thalamus to left prefrontal cortex (P = 0.023), right posterior parietal cortex (P = 0.03), and bilateral temporal cortex (left: P = 0.014; right: P = 0.015) in ASD compared with healthy control (HC) participants. The GCA values of the thalamus‐bilateral temporal cortex connections were significantly negatively correlated with communication scores as assessed by the autism diagnostic observation schedule in the ASD group (left: P = 0.037; right: P = 0.007). Age‐related analyses showed that the strengths of the thalamus‐bilateral temporal cortex connections were significantly positively correlated with age in the HC group (left: P = 0.013; right: P = 0.016), but not in the ASD group (left: P = 0.506; right: P = 0.219). These results demonstrate impaired thalamo‐cortical information transmission in ASD and suggest that atypical development of thalamus‐temporal cortex connections may relate to communication deficits in the disorder. Autism Res 2016, 9: 1183–1190. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.
Snail is critical for tumor growth and metastasis of ovarian carcinoma

Snail, a key inducer of epithelial‐mesenchymal transition (EMT), plays an important role in cancer metastasis. To better understand the role of Snail in the metastasis of ovarian carcinoma, expression of Snail was knocked down by antisense‐Snail in the highly metastatic ovarian cancer cell line HO8910PM. Gene array analysis revealed that blocking Snail expression suppressed the activity of matrix metalloproteinases (MMPs) and upregulated TIMP3, an MMP inhibitor. These findings suggest that Snail interacts with MMP during tumor invasion and metastasis. In addition, we examined the role of Snail in an ovarian cancer orthotopic model by using the antisense‐Snail HO8910PM cell line. We found that the size of primary ovarian cancer tumor and the number of metastatic lesions were significantly reduced when Snail was knocked down. Confirming our initial findings, the activity of MMP2 was greatly inhibited in tumors from antisense‐Snail cells. Furthermore, immunohistochemical analysis on ovarian cancer progression tissue array demonstrated that the expression of Snail was significantly higher in metastatic lesions, and Snail expression correlated with the stage of ovarian cancer. Interestingly, in early‐stage tumors, Snail was localized in both the cytoplasm and nucleus. In late stage and metastatic lesions, the level of Snail was elevated, and Snail was localized to the nucleus. The expression level and nuclear localization of Snail were also inversely correlated with E‐cadherin expression. Overall, our study indicates that Snail plays a critical role in tumor growth and metastasis of ovarian carcinoma through regulation of MMP activity.
Characterization of mRNA for a Proline-Rich Protein of Cotton Fiber

Cotton (Gossypium hirsutum L.) mRNA (H6) is expressed predominantly in fiber cells and is present during early primary cell wall formation. However, H6 protein is found to accumulate during later stages, when active secondary cell wall formation occurs, indicating possible regulation at the translational level and function in the secondary cell wall assembly. The nucleotide-derived amino acid sequence of pCK-H6 is proline rich (35 mol %) with a calculated molecular mass of 21 kD. Cotton protein H6 contains a repetitive pentameric motif (17) of alanine (serine)-threonine (serine)-proline-proline-proline. Its amino acid composition and solubility indicate that it may belong to the group of arabinogalactan proteins. Both sodium dodecyl sulfate-polyacrylamide gel electrophoresis (55 kD) and size-exclusion chromatography (77–83 kD) overestimated the size of in vitro synthesized H6 protein compared to the molecular mass derived from the nucleotide sequence (21 kD). The conformation of the molecule determined by its unusual primary structure may be the cause of its anomalous mobility. The presence of a proline-rich, arabinogalactan-type protein in cotton fiber raises the interesting possibility that it may be an integral part of the plasmalemma taking part in the development and architecture of the secondary wall of cotton fiber.
“Trait” and “state” aspects of fixation disparity during reading

In our study, 14 subjects read 60 sentences from the Potsdam Sentence Corpus twice (viewing distance: 60 cm), while eye movements were measured with the EyeLink II. We analyzed fixation disparities for complete sentence replications (N=388). After subtracting the average fixation disparity of each sentence from each observation (which gave the “state” fixation disparity), 99% of all remaining fixation disparities were aligned, i.e. smaller than one character width (20 min arc) – depending mostly on incoming saccade amplitude and fixation position. Additionally, we measured the heterophoria for each subject during calibration and found a qualitative relationship between average, individual measures of fixation disparity (“trait” fixation disparity) and heterophoria, after dividing the sample in 3 groups of esophore, exophore and orthophore subjects. We showed that the magnitude of “trait” fixation disparity was biased by the direction of heterophoria: the more eso the heterophoria, the more eso the average sentence fixation disparity. In sum, despite a large “trait” fixation disparity (in the range of -6.6 to +33.6 min arc), “state” fixation disparities within a sentence were on average -0.9 (± 8.7) min arc and, thus, as precise as needed, i.e. within the expected extent of Panum’s area.