Miracle-dz/UniFAR-FTUs huggingface dataset:
The binding of foot‐and‐mouth disease virus leader proteinase to eIF4GI involves conserved ionic interactions

The leader proteinase (Lpro) of foot‐and‐mouth disease virus (FMDV) initially cleaves itself from the polyprotein. Subsequently, Lpro cleaves the host proteins eukaryotic initiation factor (eIF) 4GI and 4GII. This prevents protein synthesis from capped cellular mRNAs; the viral RNA is still translated, initiating from an internal ribosome entry site. Lpro cleaves eIF4GI between residues G674 and R675. We showed previously, however, that Lpro binds to residues 640–669 of eIF4GI. Binding was substantially improved when the eIF4GI fragment contained the eIF4E binding site and eIF4E was present in the binding assay. Lpro interacts with eIF4GI via residue C133 and residues 183–195 of the C‐terminal extension. This binding domain lies about 25 Å from the active site. Here, we examined the binding of Lpro to eIF4GI fragments generated by in vitro translation to narrow the binding site down to residues 645–657 of human eIF4GI. Comparison of these amino acids with those in human eIF4GII as well as with sequences of eIF4GI from other organisms allowed us to identify two conserved basic residues (K646 and R650). Mutation of these residues was severely detrimental to Lpro binding. Similarly, comparison of the sequence between residues 183 and 195 of Lpro with those of other FMDV serotypes and equine rhinitis A virus showed that acidic residues D184 and E186 were highly conserved. Substitution of these residues in Lpro significantly reduced eIF4GI binding and cleavage without affecting self‐processing. Thus, FMDV Lpro has evolved a domain that specifically recognizes a host cell protein.
SUBCUTANEOUS PANNICULITIS-LIKE T-CELL LYMPHOMA IN A CHILD WITH TRISOMY 21

Subcutaneous Panniculitis-Like T-cell Lymphoma (SPTCL) is a rare lymphoma with fewer than twenty cases reported in children less than 18 years of age. Trisomy 21 is a chromosomal abnormality associated with a risk of malignancy that differs from their normal counterparts. Leukemia is diagnosed 10–20 times over the general population while solid tumors are underrepresented. The risk for Lymphoma historically has been elevated as well. We describe a case of a 3 year-old girl with Down syndrome who was successfully treated for SPTCL.
Feasibility of Miscanthus as alternative bedding for dairy cows

Despite dairy farmers' awareness of the importance of correct bedding for the health and comfort of their cows, they are often frugal with respect to these bedding materials in order to reduce costs. In addition, farmers are currently dependent on the availability and price fluctuations of traditional bedding materials. For these reasons, the scientific literature as well as the trade press point to an intensifying search for affordable alternative bedding materials. The aim of this study was to investigate whether Miscanthus, a woody grass that requires low input but generates high yield, could replace straw in deep little dairy cow cubicles. The cows' cubicles were lined for two consecutive 14-day periods with straw/chalk/water bedding, followed by two consecutive 14-day periods with ground- Miscanthus/chalk bedding. No significant differences were found in the following parameters: loss/ waste of bedding material, bacterial growth in cubicles, cow skin lesions (except for carpus lesions), cow cleanli - ness or cow comfort. Dust concentrations measured as PM 10 were higher when cubicles were filled with straw- based bedding, but never exceeded workspace quality safety limits. Based on these results, one can conclude that Miscanthus has potential as a viable alternative to straw when used as a bedding material. On-farm cultivation of Miscanthus may increase dairy farmer self-sufficiency and could reduce bedding costs.
DHTK: The Digital Humanities ToolKit

Digital Humanities have the merit of connecting two very different disciplines such as humanities and computer science. In this paper we present a new python library, The Digital Humanities ToolKit (DHTK), whose scope is to provide a fast and intuitive tool for a largescale study of large literary databases by leveraging on some well-known semantic knowledge resources. In addition, DHTK has the ambition to go beyond textual resources to integrate other human resources such as images (e.g., paintings, comics, etc) or sounds (e.g., music, transcripts, etc). DHTK is a collaborative project and we invite anyone who has the interest or some ideas in this context to reach out to us.
Ju l 2 00 0 Quantum phase transitions in d-wave superconductors

Motivated by the strong, low temperature damping of nodal quasiparticles observed in some cuprate superconductors, we study quantum phase transitions in dx2−y2 superconductors with a spin-singlet, zero momentum, fermion bilinear order parameter. We present a complete, group-theoretic classification of such transitions into 7 distinct cases (including cases with nematic order) and analyze fluctuations by the renormalization group. We find that only 2, the transitions to dx2−y2 + is and dx2−y2 + idxy pairing, possess stable fixed points with universal damping of nodal quasiparticles; the latter leaves the gapped quasiparticles along (1, 0), (0, 1) essentially undamped.
Quantization of the Hall conductance for general, multiparticle Schrödinger Hamiltonians.

Theorie mathematique precise de l'argument de Langhlin pour la quantification de la conductance de Hall, pour des operateurs de Schrodinger ganeraux a n particules avec des potentiels generaux: la quantification est une consequence du contenu geometrique de la conductance et est identifiable a une integrale sur la 1ere classe de Chern
C-reactive protein reassessed.

In this issue of the Journal, Danesh and colleagues report that elevated levels of C-reactive protein (CRP) are associated with only a moderate increase in the risk of coronary heart disease (CHD). 1 Although these findings are in line with those of other large studies, the independent relative risk associated with increased CRP levels is considerably less than in some earlier reports. Using a multivariate analysis, the authors found that the predictive value of CRP measurement adds relatively little to that provided by assessments of traditional risk factors. In contrast, a smaller study suggested that the CRP level could be more .
Overexpression of the FRO2 Ferric Chelate Reductase Confers Tolerance to Growth on Low Iron and Uncovers Posttranscriptional Control1

The Arabidopsis FRO2 gene encodes the low-iron-inducible ferric chelate reductase responsible for reduction of iron at the root surface. Here, we report that FRO2 and IRT1, the major transporter responsible for high-affinity iron uptake from the soil, are coordinately regulated at both the transcriptional and posttranscriptional levels. FRO2 and IRT1 are induced together following the imposition of iron starvation and are coordinately repressed following iron resupply. Steady-state mRNA levels of FRO2 and IRT1 are also coordinately regulated by zinc and cadmium. Like IRT1, FRO2 mRNA is detected in the epidermal cells of roots, consistent with its proposed role in iron uptake from the soil. FRO2 mRNA is detected at high levels in the roots and shoots of 35S-FRO2 transgenic plants. However, ferric chelate reductase activity is only elevated in the 35S-FRO2 plants under conditions of iron deficiency, indicating that FRO2 is subject to posttranscriptional regulation, as shown previously for IRT1. Finally, the 35S-FRO2 plants grow better on low iron as compared with wild-type plants, supporting the idea that reduction of ferric iron to ferrous iron is the rate-limiting step in iron uptake.
Tactile mapping of palpable abnormalities for breast cancer diagnosis

This paper presents the development of a prototype tactile mapping device (TMD) system comprised mainly of a tactile sensor array probe, a 3D camera and a force/torque sensor, which can provide the means to produce tactile maps of the breast lumps during a breast palpation. Focusing on the key tactile topology features from breast palpation such as spatial location, size and shape of the detected lesion, and the force levels used to demonstrate the palpable abnormalities, these maps can record the results of clinical breast examination with a set of pressure distribution profiles and force sensor measurements due to detected lesion. These maps will serve as an objective documentation of palpable lesions for future comparative examinations. Preliminary results of simulated experiments and limited pre-clinical evaluations of the TMD prototype have pilot-tested our hypothesis and provided solid promising data showing the feasibility of the TMD in real clinical applications.
Equity Impacts of Neoliberal Reforms: What Should the Policy Responses Be?

The final article in this special section draws together the lessons learned from the ALPS analyses and considers a range of potential policy responses. The country case studies highlight that health systems in many low- and middle-income countries are failing not only the poor but also other income groups, who are faced with wide-ranging barriers to accessing the health care they need. A key policy intervention to address these health system failures is that of challenging the status quo in relation to the public-private health care mix. There is an urgent need to strengthen public health services that have been systematically neglected over the past few decades while also regulating the worst excesses of the private health sector. Promoting a greater reliance on financing mechanisms that are progressive and that strengthen cross-subsidies in the overall health system is critical, as is ensuring that available financial and human resources are equitably allocated among geographic areas and groups. Finally, health system interventions of this nature should be supported by broader poverty-reduction strategies. Such interventions to fundamentally change ailing health systems are essential to break the vicious cycle of poverty, ill-health, and (further) impoverishment.
Flexibility in macro-scripts for computer-supported collaborative learning

In the field of computer-supported collaborative learning (CSCL), scripts are designed to support collaboration among distant learners or co-present learners whose interactions are (at least partially) mediated by a computer. The rationale of scripts is to structure collaborative learning processes in order to trigger group interactions that may be rare in free collaboration. Fixing the degree of coercion is a delicate design choice: too rigid scripts would spoil the richness of collaborative interactions; too flexible scripts would fail to induce the targeted interactions. Because of the unpredictability of how scripts will be enacted, both the teacher and the students must be allowed to modify some script features. In this article we propose a conceptual analysis of this notion of flexibility, arguing for a dissociation of constraints that are intrinsic to the pedagogical design of the script and constraints induced by the technology or contextual factors. This difference sets up the limits of flexibility both for the teacher and for the students and provides specification for the computational design. This analysis leads to the conclusion that the operationalization of CSCL scripts should be addressed by implementing script engines handling multiple representations of the script: the script to be executed, the emergent organization of teams, the set of intrinsic and extrinsic constraints and the visual representation of the script for students and teachers.
Congenital Cholesteatoma Is Predominantly Found in the Posterior-Superior Quadrant in the Asian Population: Systematic Review and Meta-analysis, Including Our Clinical Experience

Objective The study compares the clinical features of patients with congenital cholesteatoma seen in our institution over the most recent 10 years versus those seen in the previous decade. Furthermore, this study includes a systematic review and meta-analysis investigating whether differences in site predilection of congenital cholesteatoma exist between patients from Asian and Western countries. Data Sources The retrospective review consisted of 31 cases encountered from 2001 to 2011 as compared with 40 cases previously described. For systematic review, data were retrieved from PubMed, EmBase, and the Japan Medical Abstracts Society Database (January 1995 through May 2012). Study Selections Articles addressing site predilection of congenital cholesteatoma were selected with no language preference. Data Extraction The database was searched using the keywords “congenital cholesteatoma. ” After critical review of 408 studies, 27 studies were eligible for quantitative synthesis. Data Synthesis A retrospective analysis of our departmental cases showed that more than 70% (8/11) of the Potsic’s stage I or II cases had a predilection for the anterior-superior quadrant (ASQ). None of the Stage III (17) or IV (3) cases had a similar site predilection. Consistent with our previous chart review, Stage III was the most common, comprising more than 60% of cases. Meta-analysis of the 27 eligible studies provided sufficient information regarding locations of congenital cholesteatoma, and Asian studies showed less frequent ASQ involvement (overall estimate, 0.54; 95% confident interval [CI], 0.49–0.59) when compared with Western studies (overall estimate, 0.76; 95% CI, 0.73–0.80). Moreover, the involvement of posterior-superior quadrant (PSQ) in Asian studies was estimated as 0.69 (95% CI, 0.64–0.73), which was higher than that associated with involvement of ASQ. Conclusion In contrast to Western studies, PSQ was more frequently involved than ASQ in Asian studies of congenital cholesteatoma. The posteriorly located lesions might have a completely distinct pathophysiologic origin when compared with lesions originating from the ASQ.
Genetic Evidence of a Role for Lck in T-Cell Receptor Function Independent or Downstream of ZAP-70/Syk Protein Tyrosine Kinases

ABSTRACT T-cell antigen receptor (TCR) engagement results in sequential activation of the Src protein tyrosine kinases (PTKs) Lck and Fyn and the Syk PTKs, ZAP-70 and Syk. While the Src PTKs mediate the phosphorylation of TCR-associated signaling subunits and the phosphorylation and activation of the Syk PTKs, the lack of a constitutively active Syk PTK has prohibited the analysis of Lck function downstream of these initiating signaling events. We describe here the generation of an activated Syk family PTK by substituting the kinase domain of Syk for the homologous region in ZAP-70 (designated as KS for kinase swap). Expression of the KS chimera resulted in its autophosphorylation, the phosphorylation of cellular proteins, the upregulation of T-cell activation markers, and the induction of interleukin-2 gene synthesis in a TCR-independent fashion. The KS chimera and downstream ZAP-70 or Syk substrates, such as SLP-76, were still phosphorylated when expressed in Lck-deficient JCaM1.6 T cells. However, expression of the KS chimera in JCaM1.6 cells failed to rescue downstream signaling events, demonstrating a functional role for Lck beyond the activation of the ZAP-70 and Syk PTKs. These results indicate that downstream TCR signaling pathways may be differentially regulated by ZAP-70 and Lck PTKs and provide a mechanism by which effector functions may be selectively activated in response to TCR stimulation.
Missed Nursing Care, Level of Staffing, and Job Satisfaction: Lebanon Versus the United States

Missed nursing care refers to omission of standard required nursing care of patients in acute care hospitals. The objective of this study was to compare the amounts and reasons of missed nursing care, the level of nurse staffing, and job satisfaction between the United States and Lebanon. Several studies in the United States have shown that a significant amount of care is being missed. This study is designed to determine if Lebanon is experiencing a similar phenomenon and what reasons are given for missing nursing care. Findings support that a substantial amount of nursing care is missed in Lebanon, although less than that in the United States (t = 11.53, P < .001), that nurses in Lebanon were less satisfied with being a nurse than are nurses in the United States, and there was no difference in the identification of staffing resources as a reason for missed care in the 2 countries.
Sizing sampling rate of the integrated PV simulator

PV simulators are now mandatorily used to evaluate the performance of balance of system viz. battery chargers, inverters and unidirectional DC-DC simulators to avoid the time-consuming and costly field testing process. Moreover, to precisely tune the MPPT controller, we often require sustained environmental condition and status-quo for parameters; thus, PV simulators have become indispensible equipment for PV system prototyping. Further, as MPPT algorithms are more-or-less standardized, the PV simulator may be more effectively integrated with Incremental Conductance based MPPT algorithm to realize the integrated PV simulator (IPVS). Since the characteristics of each PV panel varies from manufacturer to manufacturer and parameters are selectable, the PWM frequency of buck converter used for hardware realization of IPVS and selection of an appropriate sampling rate for PV simulator for realizing the quantized digital emulation of PV panel closed to its actual operation becomes critical. This paper presents the development of a low cost microcontroller based real time IPVS which controls the interfaced buck type MPPT DC-DC power converter for emulation of PV panel close to its actual operation with flexibility or dynamic changes in characteristics. The developed algorithm is able to configure both the PV module of any make or type to its characteristics and related dynamics to be simulated and the environmental conditions under which it operates. The presented experimental results demonstrate the effectiveness of the proposed method in replicating of I-V characteristics of considered PV panel with high accuracy.
Mean Ages of Homicide Victims and Victims of Homicide–Suicide

Using Riedel and Zahn's 1994 reformatted version of an FBI database, the mean age of homicide victims in 2,175 homicide–suicides (4,350 deaths) was compared with that of all other victims of homicides reported for the USA from 1968 to 1975. The overall mean age of homicide victims in homicide–suicides was 1 yr. greater than for victims of homicides not followed by suicides, whereas the mean age for both male and female homicide–suicide victims was, respectively, 3 yr. less and greater than the other homicide victims. The mean age of Black homicide victims of homicide–suicides was 2.4 yr. less than that for Black victims of other homicides, whereas the means for Black and White male homicide victims in homicide–suicides were, respectively, about 4 and 5 yr. less than for victims of other homicides. Also, the mean age of White female homicide victims in homicide–suicides was more than two years greater than for female victims of homicides not followed by suicides. When both sex and race were considered, the mean age for those killed in homicide–suicides relative to those killed in homicides not followed by suicides may represent subpopulations with different mean ages of victims.
Neighbourhood Discriminant Embedding in face recognition

Neighborhood Preserving Embedding (NPE) is a linear approximate of Locally Linear Embedding with local geometry preserving property. An efficient face recognition method requires a mapping to separate within-class structure from between-class structure. But, NPE is not in the case since it is unsupervised. Hence, we improved NPE- utilizing the neighbor and class relations of face data. The proposed technique, Neighborhood Discriminant Embedding (NDE), takes into account the local neighboring and the between-class neighboring information. NDE seeks a projection in such that the projected samples of different classes are far apart. Experimental results show that NDE achieves superior results to NPE in face authentication with error reduction at least 20%.
Progression of fibrosis in HIV and hepatitis C virus-coinfected patients treated with interferon plus ribavirin-based therapy: analysis of risk factors.

BACKGROUND We determined the prevalence and determinants of worsening fibrosis in patients coinfected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) who were receiving anti-HCV therapy. METHODS Among 383 HIV-HCV-coinfected patients who received at least 1 dose of anti-HCV treatment (weekly subcutaneous injections of 1.5 mug/kg pegylated interferon-alpha-2b plus daily ribavirin or thrice-weekly subcutaneous injections of 3 MU of interferon-alpha-2b plus daily ribavirin for 48 weeks), paired pretreatment and posttreatment liver biopsy specimens were available and interpretable for 198 cases. Hepatic necroinflammation and fibrosis were graded with Ishak's classification. Histological worsening of fibrosis was defined as a score increase of > or =2 points in patients with fibrosis stage of <4 and as a score increase of 1 point in patients with stage-5 fibrosis. RESULTS The mean interval +/- standard deviation between the 2 biopsies was 109 +/- 34 weeks. Fibrosis worsened in 34 patients (17.1%). In univariate analysis, ongoing antiretroviral therapy, failure to achieve a sustained viral response, nucleoside reverse-transcriptase inhibitor therapy, didanosine therapy, and stavudine therapy were significantly associated with worsening of fibrosis. Didanosine (odds ratio, 3.34; 95% confidence interval, 1.39-7.96; P = .007) and failure to have a sustained viral response (odds ratio, 9.05; 95% confidence interval, 2.06-39.66; P = .003) remained significantly associated with worsening of fibrosis. CONCLUSION The mitochondrial toxicity of antiretrovirals, such as didanosine, seems to play a major role in worsening of fibrosis during HCV therapy. Therefore, anti-HCV therapy should ideally be administered before antiretroviral treatment initiation. If anti-HCV and anti-HIV treatments have to be administered concomitantly, then nucleoside reverse-transcriptase inhibitors with the lowest mitochondrial toxicity should be preferred.
Vestibulodynia (former vulvar vestibulitis): Personality in affected women

Aim. There are very few studies regarding the personality in women suffering from vestibulodynia. Our former results showed increased levels of depression and state anxiety in these women (and their partners). In order to optimize treatment of these patients we wanted to assess personality and its association with depression and anxiety. Methods. Thirty women attending the vulva clinic for the first time were included at the time of diagnosis (vestibulodynia). The Temperament and Character Inventory (TCI) was administered to assess personality, Beck's Depression Inventory (BDI) to assess depression, State Anxiety Inventory (STAI-S) to assess anxiety, and a questionnaire to assess clinical results. Results. Results showed that women with vestibulodynia have a personality profile with specific temperament and character traits. The results on the TCI temperament dimension characterized them as cautious, careful, insecure, and pessimistic. Results on the TCI character dimension indicated them to experience their own behavior and choices influenced out of their control or against their own will. The interaction of these factors may form a personality profile, resulting in an increased vulnerability in intimate relations and it could also be an important factor for state of depression and anxiety. Conclusions. The present results indicate the importance of identifying psychological factors in order to optimize the care of vestibulodynia patients and to relieve their symptoms and improve their situation. We therefore want to emphasize that vestibulodynia patients should always, in addition to medical examination and treatment, also be psychologically examined.