Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Patterns of Retinal-Binding Pockets of Type I Rhodopsins and Their Functions†

Abstract Genome sequencing projects resulted in the identification of a large number of new sequence homologs of archaeal rhodopsins in marine bacteria, fungi, and unicellular algae. It is an important task to unambiguously predict the functions of these new rhodopsins, as it is difficult to perform individual experiments on every newly discovered sequence. The transmembrane segments of rhodopsins have similar three-dimensional structures where the seven transmembrane helices form a tightly packed scaffold to accommodate a covalently bound retinal. We use geometric computations to accurately define the retinal-binding pockets in high-resolution structures of rhodopsins and to extract residues forming the wall of the retinal-binding pocket. We then obtain a tree defining the functional relationship of rhodopsins based on the short sequences of residues forming the wall of the retinal-binding pocket concatenated from the primary sequence, and show that these sequence fragments are often sufficient to discriminate phototactic vs transporting function of the bacterial and unicellular algal rhodopsins. We further study the evolutionary history of retinal-binding pockets by estimating the pocket residue substitution rates using a Bayesian Monte Carlo method. Our findings indicate that every functional class of rhodopsins has a specific allowed set of fast-rate amino acid substitutions in the retinal-binding pocket that may contribute to spectral tuning or photocycle modulation. The substitution rates of the amino acid residues in a putative retinal-binding pocket of marine proteorhodopsins together with the clustering of pocket sequences indicate that green-absorbing and blue-absorbing proteorhodopsins have similar function. Our results demonstrate that the evolutionary patterns of the retinal-binding pockets reflect the functional specificity of the rhodopsins. The approach we describe in this paper may be useful for large-scale functional prediction of rhodopsins.
A patient with systemic lupus erythematosus who developed massive small intestinal hemorrhaging during treatment for chronic lupus peritonitis

A 50-year-old Japanese woman, a patient with systemic lupus erythematosus (SLE) complicated with chronic lupus peritonitis, developed massive small intestinal hemorrhaging. She was treated with intravenous pulse of methylprednisolone, intravenous pulse of cyclophosphamide (IVCY), and immunoabsorption, but the peritonitis was refractory to these treatments. Subsequently, she was treated with oral corticosteroid and tacrolimus, and received IVCY monthly, but she developed massive small intestinal hemorrhaging 1 year after. Abdominal angiography detected multiple bleeding sites from the jejunal and ileal arteries. After transarterial embolization treatment, the melena disappeared. The pathology of this case appeared to be lupus mesenteric vasculitis.
Smallpox Bioterror Response

In their report “Containing bioterrorist smallpox” (15 Nov., p. [1428][1]), M. E. Halloran et al. state that their “structured simulator” does not produce the “two orders of magnitude difference” between the number of deaths under targeted vaccination and the number of deaths under mass
Emerging drug therapies in Huntington's disease

Huntington's disease (HD) is a relentless neurodegenerative disease that results in profound disability through a triad of motor, cognitive and neuropsychiatric symptoms. At present, there are very few therapeutic interventions available with the exception of a limited number of drugs that offer mild symptomatic relief. Although the genetic basis of the disease has been identified, the mechanisms behind the cellular pathogenesis are still not clear and as a result no candidate drugs with the potential for disease modification have been found clinically until now. One of the major limitations in assessing the usefulness of drug treatments in HD is the lack of well-designed, double-blind, placebo-controlled clinical trials. Most studies have been open-label, using a small number of patients and tend to concentrate on the motor features of the disease, primarily the chorea. This review discusses the treatments now used for HD before evaluating the newer drugs at present being explored in both the clinic and in the laboratory in mouse models of the disease.
Psychologically mediated abdominal pain in surgical and medical outpatients clinics.

Ninety-six patients complaining of recurrent or persistent abdominal pain were referred consecutively to a surgical clinic and a medical clinic, respectively. They were examined psychiatrically after their initial physical investigation. The psychiatric examination included rating scales for depression and anxiety, a personality inventory, life-events schedule, scale of verbal expressivity, and family and personal patterns of pain and invalidism. Only 15 patients (15-6%) had organic disorders that could be responsible for their symptoms. In the remainder, psychiatric factors were considered primarily responsible for their abdominal pain: 31 were depressed; 21 had chronic tension; in 17 hysterical mechanisms were prominent; and 12 were found to be unrecognised alcoholics. Follow-up at three and six months and recognition by 80% of the psychogenic group that a psychological explanation was plausible, confirmed the diagnoses, and over half responded favourably to psychiatric management. Features distinguishing the organic and psychogenic groups were delineated. Psychiatric assessment has a place among the investigations of non-acute abdominal pain; certainly it should not be condisered simply as "a last resort. "
QoE Content Distribution Network for Cloud Architecture

Cloud Service has become now a real trend in the development of network services. It is a concept of deporting resources and services on remote servers as opposed to traditional hosting on the user workstation. In fact, cloud services require more bandwidth due to high quality media. Content Distribution Network (CDN) with a mechanism of replication of information among multiple servers is a solution to support high request volume and ameliorate network quality. Integrating Cloud concept into Content Distribution Network (CDN) is an effective approach to improve network quality. In this paper, we propose a Content Distribution Network Cloud Architecture (CDNCA). Our approach is based not only on Quality of Service criteria (QoS) (e.g. round trip time, network hops, loss rate, etc.) but also on the Quality of Experience that represents end-users perception and satisfaction. Experimental results show that CDNCA yields significant improvements over traditional approaches.
Ordering systems: coordinative practices in architectural design and planning

In their cooperative effort, architects depend critically on elaborate coordinative practices and artifacts. The paper presents, on the basis of an in-depth study of architectural work, an analysis of these practices and artifacts and shows that they are multilaterally interrelated and form complexes of interrelated practices and artifacts which we have dubbed 'ordering systems'. In doing so, the paper outlines a conceptual framework for investigating and conceiving of such practices.
The effect of protein II and pili on the interaction of Neisseria gonorrhoeae with human polymorphonuclear leucocytes.

Colonial variants of Neisseria gonorrhoeae strain P9 expressing different pili and/or outer membrane protein II (P.II) were investigated with respect to their interaction with human polymorphonuclear leucocytes (PMN). Two assay systems were used. A phagocytic killing assay measured the intracellular survival of gonococci, and PMN chemiluminescence (CL) was used to determine the initial surface interactions. All variants expressing P.II were killed effectively by PMN and also greatly stimulated PMN CL. The P.II- variants, on the other hand, were resistant to phagocytic killing and stimulated a much lower CL response. The presence of different P.II species was associated with different CL profiles and therefore different modes of interaction with the PMN membrane. A P.II-specific monoclonal IgG was opsonic and greatly increased PMN CL in contrast to F(ab')2 prepared from the same antibody, which inhibited it, thus confirming the role of P.II in the PMN interaction. Phagocytic killing assays revealed that with the loss of P.II, gonococcal variants acquired resistance to killing. Comparison of piliated and non-piliated pairs of variants with the same P.II profile showed that PMN-gonococcal interactions are dominated by the nature of the P.II species present whereas pili have little effect.
Impact of reading a scientific journal issue about hypnosis on the beliefs and attitudes towards hypnosis among psychologists

The goal of this study was to examine the influence of receiving scientific information about hypnosis over Spanish psychologists' beliefs and attitudes toward hypnosis. The Valencia Scale on Attitudes and Beliefs toward Hypnosis-Therapist (VSABH-T) was administered to 2434 Spanish psychologists. A retest and a second retest were carried out, and between these testing administrations a monograph issue focused on hypnosis was published in a journal that all members of the Spanish Psychological Association received. Results indicated that psychologists who read this monograph, in general terms, changed their misconceptions about hypnosis for correct beliefs and their negative attitudes toward hypnosis for positive ones. Moreover, the VSABH-T was useful for detecting changes in psychologists' beliefs and attitudes toward hypnosis.
From Equivalence of Standards to Equivalence of Objectives: The Entitlement of Prisoners to Health Care Standards Higher than Those Outside Prisons

It is generally accepted that people in prison have a right to a standard of health care equivalent to that available outside of prisons. This ‘‘principle of equivalence’’ is one that enjoys broad consensus among international health and human rights instruments and organisations. However, given the extreme health problems evident in prisons worldwide, the legal obligations of the State to safeguard the lives and well-being of people it holds in custody and the implications of poor prison health on overall public health, this article suggests that – even if achieved - standards of prison health care only equivalent to that in the community would in some cases fall short of human rights obligations and public health needs. The article argues it is time to move beyond the concept of equivalent standards of health care, and instead promote standards that achieve equivalent objectives. In some circumstances, meeting this new standard will require that the scope and accessibility of prison health services are higher than that outside of prisons.
PAPR Reduction for OFDM Systems by Deliberate Power Boost

In this paper, we propose deliberate power boost (DPB) to reduce the PAPR (peak-to-average power ratio) in an OFDM (orthogonal frequency-division multiplexing) system. Although both the average power and peak power are increased by using DPB, we show that the PAPR can be reduced by the proposed method. DPB can be combined with other PAPR-reduction techniques such as deliberate clipping and repeated clipping and filtering (RCF) for further PAPR reduction. Although selective mapping (SLM) is originally proposed for PAPR reduction, we apply a concept similar to SLM to clipping-based OFDM systems for improved error performance. We show that turbo coded OFDM systems using both RCF and DPB can achieve better PAPR performance without degrading the error performance as compared to the case of using only RCF if SLM is used for improved error performance in both systems.
Reflective Writing: Quantitative Assessment and Identification of Linguistic Features

Reflective writing is used in higher education to encourage students to reflect on their learning or practice; in this context, reflective writing is frequently assessed. However, not enough is known about the criteria that educators use when assessing reflection. Many studies have developed rubrics for reflective writing assessment but these instruments are based on broad qualitative criteria and make no attempt to quantify depth of reflection. In addition to this, little is known about the linguistic structure of reflective writing; although some recent studies have examined its features, these characteristics have not been correlated to levels of reflective depth. Also of concern are the ways in which technology can impact the reflective writing and assessment process. Although many studies tout the benefits of using reflective blogging in higher education there is a dearth of empirical data that compares the effectiveness of blogging with more traditional ‘offline’ journals. A Delphi study was conducted with a group of international Reflective Practice experts to determine the criteria they use to assess reflective writing. The first round of the study identified 12 indicators of reflection; in the second round experts ranked these indicators according to depth of reflection. The reflection indicators form the basis of an instrument that can be used to assign a quantitative score to a piece of reflective writing based on the depth of reflection it contains. This instrument was used to perform a content analysis on the academic reflective writing contained in 27 reflective blogs and journals. The linguistic resources used in students’ writing were also assessed. A strong correlation was found between the overall reflective score and the total number of linguistic resources used, showing that reflective writing tends to be linguistically richer. In addition to this, relationships were seen between specific features of reflective writing and levels of reflection. A reflective scoresheet was developed that maps reflective writing assessment criteria to expected linguistic resources. This new understanding of the structure of reflective writing also has implications for the fields of automated writing evaluation and intelligent tutoring. The study also compared the writing in blogs and journals and found no significant difference in the linguistic resources they utilised, showing that the type of language used is the same, regardless of medium. A correlation was seen between the provision of feedback and improvement in reflective writing over time. A model of the reflective writing and assessment process that describes how blogs can be used to support the provision of regular formative feedback was presented.
Biologically relevant mechanism for catalytic superoxide removal by simple manganese compounds

Nonenzymatic manganese was first shown to provide protection against superoxide toxicity in vivo in 1981, but the chemical mechanism responsible for this protection subsequently became controversial due to conflicting reports concerning the ability of Mn to catalyze superoxide disproportionation in vitro. In a recent communication, we reported that low concentrations of a simple Mn phosphate salt under physiologically relevant conditions will indeed catalyze superoxide disproportionation in vitro. We report now that two of the four Mn complexes that are expected to be most abundant in vivo, Mn phosphate and Mn carbonate, can catalyze superoxide disproportionation at physiologically relevant concentrations and pH, whereas Mn pyrophosphate and citrate complexes cannot. Additionally, the chemical mechanisms of these reactions have been studied in detail, and the rates of reactions of the catalytic removal of superoxide by Mn phosphate and carbonate have been modeled. Physiologically relevant concentrations of these compounds were found to be sufficient to mimic an effective concentration of enzymatic superoxide dismutase found in vivo. This mechanism provides a likely explanation as to how Mn combats superoxide stress in cellular systems.
Optimum power allocation for parallel Gaussian channels with arbitrary input distributions

The mutual information of independent parallel Gaussian-noise channels is maximized, under an average power constraint, by independent Gaussian inputs whose power is allocated according to the waterfilling policy. In practice, discrete signaling constellations with limited peak-to-average ratios (m-PSK, m-QAM, etc.) are used in lieu of the ideal Gaussian signals. This paper gives the power allocation policy that maximizes the mutual information over parallel channels with arbitrary input distributions. Such policy admits a graphical interpretation, referred to as mercury/waterfilling, which generalizes the waterfilling solution and allows retaining some of its intuition. The relationship between mutual information of Gaussian channels and nonlinear minimum mean-square error (MMSE) proves key to solving the power allocation problem.
Politeness, culture, and speaking task – paralinguistic prosodic behavior of speakers from Austria and Germany

This paper tests previous findings for polite speech of low pitch, low intensity, higher number of hesitation markers and filled pauses against those parameters in a different socio-cultural background. Two similar groups of (19+13) participants, from Austria and from Germany, were recorded. The adopted experimental approach used 16 tasks aiming at different speech acts in situations that evoke either polite or informal speech. The analyzed acoustic and electroglottographic signals reveal main effects for lower pitch, lower intensity and HNR only for the German group. Open quotient values differ only for female speakers. In both groups significantly lower word rate and lower speaking rate as well as higher rates of filled pauses and hesitation markers are found in formal (polite) conditions. However individual speakers can show indifferent or opposing behavior for a given parameter with compensatory utilisation of other parameters in order to express politeness (formality).
Impaired face and body perception in developmental prosopagnosia

Prosopagnosia is a deficit in face recognition in the presence of relatively normal object recognition. Together with older lesion studies, recent brain-imaging results provide evidence for the closely related representations of faces and objects and, more recently, for brain areas sensitive to faces and bodies. This evidence raises the issue of whether developmental prosopagnosics may also have an impairment in encoding bodies. We investigated the first stages of face, body, and object perception in four developmental prosopagnosics by comparing event-related potentials to canonically and upside-down presented stimuli. Normal configural encoding was absent in three of four developmental prosopagnosics for faces at the P1 and for both faces and bodies at the N170 component. Our results demonstrate that prosopagnosics do not have this normal processing routine readily available for faces or bodies. A profound face recognition deficit characteristic of developmental prosopagnosia may not necessarily originate in a category-specific face recognition deficit in the initial stages of development. It may also have its roots in anomalous processing of the configuration, a visual routine that is important for other stimuli besides faces. Faces and bodies trigger configuration-based visual strategies that are crucial in initial stages of stimulus encoding but also serve to bootstrap the acquisition of more feature-based visual skills that progressively build up in the course of development.
Changes in the clinical features of child and adolescent psychiatric inpatients: a nationwide time-trend study from Finland

Background: Few studies have focused on the recent trends in clinical features child and adolescent inpatient. Aims: This study focuses on the change in the characteristics of child and adolescent psychiatric inpatients in Finland. Methods: The data collection was carried out on selected study days in 2000 and 2011. Questionnaires were sent to the psychiatrists of all child and adolescent wards in Finland. Results: By comparing the data obtained in 2000 (n = 504) and 2011 (n = 412), several changes were found: the percentage of girls in adolescent wards grew and the diagnoses of depression, anxiety disorders, attention deficit hyperactivity disorder and eating disorders increased. In contrast, the diagnoses of psychosis and conduct or oppositional disorders decreased. General functioning was evaluated with the Childreńs Global Assessment Scale (CGAS). There were no changes in the distribution of CGAS scores among child inpatients, whereas among adolescents the share of inpatients with lowest CGAS scores (1–30) increased significantly. The mean length of stay dropped. Conclusions: The growing percentage of girls in adolescent wards is associated with an increase in diagnoses that are more prevalent among girls than boys, namely depression, anxiety, and eating disorders. The changes in the distribution of diagnoses may be due to changes in diagnostic or referral practices, or reflect true changes in the prevalence of disorders among children and adolescents in need of inpatient treatment. The share of adolescent inpatients with the poorest general functioning has increased. The observed shortening in inpatient treatment time seems to be a result of changes in treatment practices.
Blood spot screening and confirmatory tests for syphilis antibody

We developed a blood spot test for syphilis antibody using enzyme-linked immunosorbent assay (ELISA) technology. Dried blood was eluted by buffered saline or, for a supplementary confirmatory test, by treponemal-antibody test diluent. Eluates were diluted in an absorption buffer (Calypte Biomedical, Berkeley, Calif.) and added to plate wells coated with cardiolipin antigen (ADI Diagnostics, Toronto, Ontario, Canada). The wells were washed and treated sequentially with an immunoglobulin G conjugate, buffer washes, and enzyme substrate. Substrate conversion was measured photometrically, and specimen reactivity was determined by reference to nonreactive controls. The optimum test protocol was established by tests of serum and plasma. The serum ELISA specificity with normal specimens was 98.9%. The sensitivity with sera from patients with undefined syphilis was 97.4%, that with sera from patients with documented primary and secondary disease was 100%, and that with sera from patients with early and late latent disease was 95.7%. The specificity of the spot test with donor blood was 94.2%, and its specificity with newborn blood was 94.9%. The sensitivity with 25 spots spiked with reactive sera was 96%. The seroprevalence rates for parturient women in one hospital were 6.01% according to spot tests of sera from 599 newborns and 6.81% according to Rapid Plasma Reagin tests of 499 maternal serum specimens. Seventy percent of infants born to 50 seropositive women were reactive by either the newborn spot or the Rapid Plasma Reagin serum test. The results show that blood spots may be used in seroprevalence or serodiagnostic studies, especially to identify women who are infected or to identify possible cases of congenital infection. The test provides for studies of children and adults when routine venipuncture and serum handling and storage are problematic.