Miracle-dz/UniFAR-FTUs huggingface dataset:
From Mice to Men - 24 Years of Evaluation in CHI

This paper analyzes trends in the approach to evaluation taken by CHI papers in the last 24 years. A set of papers was analyzed according to our schema for classifying type of evaluation. Our analysis traces papers’ trend in type and scope of evaluation. Findings include an increase in the proportion of papers that include evaluation, and a decrease in the median number of subjects in quantitative studies. We also critique the types of subjects, in particular an over reliance on students, and lack of appropriately gender balanced samples. We contextualize these findings in historical trends as we move from machines intended for the technical elite in laboratories to computers integrated into the daily life of everyone.
Engagement of ICAM-3 Provides a Costimulatory Signal for Human Immunodeficiency Virus Type 1 Replication in both Activated and Quiescent CD4+ T Lymphocytes: Implications for Virus Pathogenesis

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) replication is regulated by several extracellular signals. We demonstrate that intercellular adhesion molecule 3 (ICAM-3) acts as a costimulating molecule to increase HIV-1 transcription and viral production, a process allowing productive infection of quiescent CD4+ T lymphocytes. The present work suggests an important role for ICAM-3 in HIV-1 replication.
A fast and accurate instruction-oriented processor simulation approach

This paper proposes an efficient instruction-oriented approach to improve processor simulation speed while maintaining perfect timing accuracy. Unlike traditional approaches, we simulate only necessary states instruction-by-instruction, instead of updating all states cycle-by-cycle. This approach can be applied to various types of processors, including superscalar processors. The experimental result shows that the simulation performance is about twenty times faster than the traditional Cycle-Accurate approach while with 100% timing accuracy.
Chapter 32. Prevention of Contrast-Induced Nephropathy

Radiocontrast-induced nephropathy (RCIN) represents an increasingly common cause of treatment-related renal failure and increases mortality independent of other risk factors. Major risk factors for RCIN include chronic renal insufficiency, diabetes mellitus (especially when accompanied by renal insufficiency), any condition associated with decreased effective circulating volume, and use of large doses of contrast media. For at-risk patients, clinicians must use their judgment to determine if imaging modalities that do not involve contrast media are an acceptable alternative to contrast studies. In many cases, however, such alternatives do not exist. Moreover, RCIN occurs in patients without obvious risk factors. Thus, strategies for reducing the incidence of RCIN include not just risk factor identification, but modification of these risk factors, choice of contrast media less likely to cause RCIN, and administration of therapeutic agents that further reduce the risk of RCIN.
Adaptive stabilization of a class of nonlinear systems with unstable internal dynamics

The paper considers global stabilization of a class of uncertain nonlinear output feedback systems with unstable internal dynamics. The coefficients which characterize the internal dynamics are allowed to be functions of system output, and the uncertainty of the system is characterized by a unknown constant parameter vector. The key step in the proposed control design is to estimate the internal state variables and impose control over them. The control design is presented first for systems without unknown parameters, and then for the systems with unknown parameters using adaptive control techniques.
Fine-tuning convolutional deep features for MRI based brain tumor classification

Prediction of survival time from brain tumor magnetic resonance images (MRI) is not commonly performed and would ordinarily be a time consuming process. However, current cross-sectional imaging techniques, particularly MRI, can be used to generate many features that may provide information on the patient’s prognosis, including survival. This information can potentially be used to identify individuals who would benefit from more aggressive therapy. Rather than using pre-defined and hand-engineered features as with current radiomics methods, we investigated the use of deep features extracted from pre-trained convolutional neural networks (CNNs) in predicting survival time. We also provide evidence for the power of domain specific fine-tuning in improving the performance of a pre-trained CNN’s, even though our data set is small. We fine-tuned a CNN initially trained on a large natural image recognition dataset (Imagenet ILSVRC) and transferred the learned feature representations to the survival time prediction task, obtaining over 81% accuracy in a leave one out cross validation.
Generalized Cox-Ross-Rubinstein Binomial Models

This paper generalizes the seminal Cox-Ross-Rubinstein (CRR) binomial model by adding a stretch parameter. The generalized CRR (GCRR) model allows us to fine-tune (via the stretch parameter) the lattice structure so as to efficiently price a range of options, such as barrier options. Our analysis provides insights into the fine structure of convergence of the general binomial model to the Black-Scholes formula. We also discuss how to improve the rate of convergence or the oscillatory behavior of the GCRR model. The numerical results suggest that the GCRR models with various modifications are efficient for pricing a range of options.
A Novel Allele of Saccharomyces cerevisiae NDC1 Reveals a Potential Role for the Spindle Pole Body Component Ndc1p in Nuclear Pore Assembly

ABSTRACT Both the spindle pole body (SPB) and the nuclear pore complex (NPC) are essential organelles embedded in the nuclear envelope throughout the life cycle of the budding yeast Saccharomyces cerevisiae. However, the mechanism by which these two multisubunit structures are inserted into the nuclear envelope during their biogenesis is not well understood. We have previously shown that Ndc1p is the only known integral membrane protein that localizes to both the SPBs and the NPCs and is required for SPB duplication. For this study, we generated a novel temperature-sensitive (ts) allele of NDC1 to investigate the role of Ndc1p at the NPCs. Yeast cells carrying this allele (ndc1-39) failed to insert the SPB into the nuclear envelope at the restrictive temperature. Importantly, the double mutation of ndc1-39 and NPC assembly mutant nic96-1 resulted in cells with enhanced growth defects. While nuclear protein import and NPC distribution in the nuclear envelope were unaffected, ndc1-39 mutants failed to properly incorporate the nucleoporin Nup49p into NPCs. These results provide evidence that Ndc1p is required for NPC assembly in addition to its role in SPB duplication. We postulate that Ndc1p is crucial for the biogenesis of both the SPBs and the NPCs at the step of insertion into the nuclear envelope.
Three‐dimensional neural differentiation of embryonic stem cells with ACM induction in microfibrous matrices in bioreactors

The clinical use of pluripotent stem cell (PSC)‐derived neural cells requires an efficient differentiation process for mass production in a bioreactor. Toward this goal, neural differentiation of murine embryonic stem cells (ESCs) in three‐dimensional (3D) polyethylene terephthalate microfibrous matrices was investigated in this study. To streamline the process and provide a platform for process integration, the neural differentiation of ESCs was induced with astrocyte‐conditioned medium without the formation of embryoid bodies, starting from undifferentiated ESC aggregates expanded in a suspension bioreactor. The 3D neural differentiation was able to generate a complex neural network in the matrices. When compared to 2D differentiation, 3D differentiation in microfibrous matrices resulted in a higher percentage of nestin‐positive cells (68% vs. 54%) and upregulated gene expressions of nestin, Nurr1, and tyrosine hydroxylase. High purity of neural differentiation in 3D microfibrous matrix was also demonstrated in a spinner bioreactor with 74% nestin + cells. This study demonstrated the feasibility of a scalable process based on 3D differentiation in microfibrous matrices for the production of ESC‐derived neural cells. © 2013 American Institute of Chemical Engineers Biotechnol. Prog. , 29:1013–1022, 2013
Risk assessment of toxic metals in marine sediments from the Arctic Ocean using a modified BCR sequential extraction procedure

ABSTRACT Surface sediment samples were collected from the Pacific sector of the Arctic Ocean during the 6th Chinese National Arctic Research Expedition (CHINARE), 2014. Concentrations and extractabilities of six toxic metals (Cd, Cr, Cu, Ni, Pb, and Zn) were determined using a modified sequential extraction procedure as described by the European Community Bureau of Reference (BCR). A new analytical hierarchy approach to risk assessment, involving sediment quality guidelines and risk-assessment codes, is described for metals in marine sediments from the Arctic Ocean. Results indicate a mobility order of Pb > Cd > Cu > Zn > Ni > Cr with mean liable fraction (F1+F2+F3) being 83.0%, 81.6%, 62.0%, 47.1%, 42.1%, and 15.6%, respectively. Ni presents the most serious ecological risk in the study area, with most samples (93.9%) indicating medium risk, followed by Cu (54.5%) and Zn (27.3%). For Ni and Zn, there are also samples showing high ecological risk (Ni at site NB02, northern Bering Sea; Zn at R07, northern Chukchi Sea). The ecological risk for Cr indicates low ecological risk (93.9%) and some medium risk (6.1%). All Cd assessments indicate low ecological risk, while most Pb assessments indicate zero (33.3%) to low risk. The new ecological risk assessment method improves on assessments based on metal mobility or concentration alone.
Nonlinear Metric Learning with Deep Independent Subspace Analysis Network for Face Verification

Face verification is the task of determining whether two given face images represent the same person or not. It is a very challenging task, as the face images, captured in the uncontrolled environments, may have large variations in illumination, expression, pose, background, etc. The crucial problem is how to compute the similarity of two face images. Metric learning has provided a viable solution to this problem. Until now, many metric learning algorithms have been propos'ed, but they are usually limited to learning a linear transformation In this paper, we propose a nonlinear metric learning method, which learns an explicit mapping from the original space to an optimal subspace using deep Independent Subspace Analysis (ISA) network. Compared to the linear or kernel based metric learning methods, the proposed deep ISA network is a deep and local learning architecture, and therefore exhibits more powerful ability to learn the nature of highly variable dataset. We evaluate our method on the Labeled Faces in the Wild dataset, and results show superior performance over some state-of-the-art methods.
Disjunctive bases: normal forms and model theory for modal logics

We present the concept of a disjunctive basis as a generic framework for normal forms in modal logic based on coalgebra. Disjunctive bases were defined in previous work on completeness for modal fixpoint logics, where they played a central role in the proof of a generic completeness theorem for coalgebraic mu-calculi. Believing the concept has a much wider significance, here we investigate it more thoroughly in its own right. We show that the presence of a disjunctive basis at the "one-step" level entails a number of good properties for a coalgebraic mu-calculus, in particular, a simulation theorem showing that every alternating automaton can be transformed into an equivalent nondeterministic one. Based on this, we prove a Lyndon theorem for the full fixpoint logic, its fixpoint-free fragment and its one-step fragment, a Uniform Interpolation result, for both the full mu-calculus and its fixpoint-free fragment, and a Janin-Walukiewicz-style characterization theorem for the mu-calculus under slightly stronger assumptions. We also raise the questions, when a disjunctive basis exists, and how disjunctive bases are related to Moss' coalgebraic "nabla" modalities. Nabla formulas provide disjunctive bases for many coalgebraic modal logics, but there are cases where disjunctive bases give useful normal forms even when nabla formulas fail to do so, our prime example being graded modal logic. We also show that disjunctive bases are preserved by forming sums, products and compositions of coalgebraic modal logics, providing tools for modular construction of modal logics admitting disjunctive bases. Finally, we consider the problem of giving a category-theoretic formulation of disjunctive bases, and provide a partial solution.
Resistance to Penicillin and Erythromycin in Viridans Streptococcal Bloodstream Isolates From Cancer and Non-Cancer Patients Within 10 Years

ed, including 333 students and 228 control subjects. Detailed results are presented in the table. The overall estimated prevalence of MRSA carriage was 2.5%, which was high when compared with the rate recorded for HCWs from countries displaying a low MRSA endemicity in hospitals. Regarding the student population, no statistical association was found between nasal carriage of MRSA and any of the items listed above and recorded through the questionnaire. In addition, no significant statistical difference in the prevalence of either methicillin-susceptible S. aureus or MRSA nasal carriage was found between students and control subjects. This study, performed during a non-epidemic period, did not confirm the high prevalence of MRSA nasal carriage observed in students of our hospital during previous epidemic periods. The results displayed in the table indicate that the two populations with the higher prevalence of MRSA nasal carriage were practitioners and fellows. When these two categories were compared with the other HCWs, a trend toward a significant statistical difference was observed (P = .07 by Fisher's exact test). Actually, compliance with handwashing and hand antisepsis was shown to be poor in this population. The latter observation suggests targeting physicians for audit of hygienic practices and information on hand antisepsis. R E F E R E N C E S 1. Berthelot P, Grattard F, Fascia P, et al. Implication of a healthcare worker with chronic skin disease in the transmission of an epidemic strain of methicillin-resistant Staphylococcus aureus in a pediatric intensive care unit. Infect Control Hosp Epidemiol 2003;24:299-300. 2. Fascia P Martin I, Mallaval FO, et al. Possible implication of student nurses in the transmission of methicillin-resistant Staphylococcus aureus during a nosocomial outbreak [in French]. Pathol Biol (Paris) 2003;51:479482. 3. Stubbs E, Pegler M, Vickery A, Harbour C. Nasal carriage of Staphylococcus aureus in Australian (pre-clinical and clinical) medical students. J Hosp Infect 1994;27:127-134. 4. Kingdom JC, Joyce SM, Bradley FL, Jauch W, Falkiner FR, Keane CT. Staphylococcal nasal carriage in medical students with varying clinical exposure. Infect Control Hosp Epidemiol 2003;24:456-458. 5. Pittet D, Hugonnet S, Harbarth S, et al. Effectiveness of a hospital-wide program to improve compliance with hand hygiene. Lancet 2000;356:1307-1312.
Visual restoration and transplant connectivity in degenerate rats implanted with retinal progenitor sheets

The aim of this study was to determine whether retinal progenitor layer transplants form synaptic connections with the host and restore vision. Donor retinal sheets, isolated from embryonic day 19 rat fetuses expressing human placental alkaline phosphatase (hPAP), were transplanted to the subretinal space of 18 S334ter‐3 rats with fast retinal degeneration at the age of 0.8–1.3 months. Recipients were killed at the age of 1.6–11.8 months. Frozen sections were analysed by confocal immunohistochemistry for the donor cell label hPAP and synaptic markers. Vibratome slices were stained for hPAP, and processed for electron microscopy. Visual responses were recorded by electrophysiology from the superior colliculus (SC) in 12 rats at the age of 5.3–11.8 months. All recorded transplanted rats had restored or preserved visual responses in the SC corresponding to the transplant location in the retina, with thresholds between −2.8 and −3.4 log cd/m2. No such responses were found in age‐matched S334ter‐3 rats without transplants, or in those with sham surgery. Donor cells and processes were identified in the host by light and electron microscopy. Transplant processes penetrated the inner host retina in spite of occasional glial barriers between transplant and host. Labeled neuronal processes were found in the host inner plexiform layer, and formed apparent synapses with unlabeled cells, presumably of host origin. In conclusion, synaptic connections between graft and host cells, together with visual responses from corresponding locations in the brain, support the hypothesis that functional connections develop following transplantation of retinal layers into rodent models of retinal degeneration.
The location of projection neurons to the biceps brachii muscle in the telencephalon of the pigeon

Few studies regarding the anatomical distribution of motor neurons innervating muscles of the arm have been demonstrated in avian brains. The purpose of this study was to finely determine the localization of cerebral neurons innervating the biceps brachii muscle in the pigeon. The cholera toxin B subunit (CTB) was employed as a retrograde tracer to determine the location of neurons controlling the biceps brachii muscle in the telencephalon following intramuscular injection in male pigeons (n = 7), which were killed 14 days after intramuscular injection with CTB. We found that CTB‐labelled neurons were located contralaterally in the hyperpallium apicale of the rostral telencephalon and that most of the CTB‐labelled neurons were pyramidal in shape. This study shows that CTB is easily taken up by nerve terminals which innervate the biceps brachii muscle of the pigeon and that cerebral motor neurons controlling the biceps brachii muscle are located in the hyperpallium apicale.
Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine kinase photoreceptor

Rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. Light, oxygen, and voltage (LOV)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. The genome of R. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a LOV domain at the N-terminal end (R-LOV-HK). R-LOV-HK has a typical LOV domain absorption spectrum with broad bands in the blue and UV-A regions and shows a truncated photocycle. Here we show that the R-LOV-HK protein regulates attachment to an abiotic surface and production of flagellar proteins and exopolysaccharide in response to light. Also, illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids. The effects of light on nodulation are dependent on a functional lov gene. The results presented in this work suggest that light, sensed by R-LOV-HK, is an important environmental factor that controls adaptive responses and the symbiotic efficiency of R. leguminosarum.
Histopathologic findings in the sacrocaudalis dorsalis medialis muscle of horses with vitamin E-responsive muscle atrophy and weakness.

OBJECTIVE To characterize clinical findings, outcomes, muscle characteristics, and serum or muscle concentrations of α-tocopherol for horses with vitamin E-responsive signs of muscle atrophy and weakness consistent with signs of equine motor neuron disease (EMND). DESIGN Retrospective case-control study. ANIMALS 8 affected (case) adult horses with acute (n = 3) or chronic (5) gross muscle atrophy that improved with vitamin E treatment and 14 clinically normal (control) adult horses with adequate (within reference range; 8) or low (6) muscle concentrations of α-tocopherol. PROCEDURES Medical records were reviewed, serum and muscle concentrations of α-tocopherol were measured, and frozen biopsy specimens of sacrocaudalis dorsalis medialis muscle and gluteal muscle were histologically evaluated for pathological changes. Fiber type composition and fiber diameters were assessed in gluteal muscle specimens. RESULTS A myopathy that was histologically characterized by redistribution of mitochondrial enzyme stain (moth-eaten appearance) and anguloid atrophy of myofibers was evident in sacrocaudalis dorsalis medialis muscle fibers of the 8 affected horses that had low serum (6/8) or skeletal muscle (5/5) concentrations of α-tocopherol; these histopathologic changes were not found in muscle specimens of control horses with low or adequate muscle concentrations of α-tocopherol. All affected horses regained strength and muscle mass within 3 months after initiation of vitamin E treatment and dietary changes. CONCLUSIONS AND CLINICAL RELEVANCE A vitamin E-deficient myopathy characterized histologically by a moth-eaten appearance in the mitochondria and anguloid myofiber atrophy in frozen sections of sacrocaudalis dorsalis medialis muscle biopsy specimens was found in horses with clinical signs of EMND that were highly responsive to vitamin E treatment. This myopathy may be a specific syndrome or possibly precede the development of neurogenic muscle fiber atrophy typical of EMND.
Molecular typing for the MHC with PCR-SSP.

Sequence-specific amplification (SSP) is simply a form of polymerase chain reaction (PCR) which involves designing one or both primers so that they will or will not allow amplification (the 3'-mismatch principle). Its origins are probably legion, i.e. many people probably thought of it at the same time. For example, in 1988 a group from Guy's Hospital, London, described a form of SSP for HLA-DR4 detection and in the same year a group from Upjohn described its use at the American Society of Histocompatibility and Immunogenetics (ASHI). Both are published in abstract form (British Society of Rheumatology and ASHI). The 3'-mismatch principle can be used to identify virtually any single nucleotide point mutation (SNP) within one or two PCR-SSP reactions and the first peer-reviewed statements of this came in 1989 (1, 2). Thus, although the use of SSP probably began around 1990, it was 5 years before its popularity erupted, mainly due to the work of Olerup & Zetterquist (3, 4), who defined its potential for solid organ transplantation. It is now the method of choice for high resolution HLA typing in many laboratories. In addition, over a thousand applications for genes outside the MHC are in the literature.