Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Infectious Diseases Consultation on Mortality of Cryptococcal Infection in Patients Without HIV

Background An infectious disease (ID) consultation is often obtained to treat patients with cryptococcosis due to the complex nature of the disease, but has never been demonstrated to impact outcomes. Methods We assembled a retrospective cohort of 147 consecutive cases of cryptococcosis in patients without HIV. Patients who were diagnosed less than 24 hours prior to death were excluded. Survival analysis was performed with Cox regression with survival censored past 90 days. Results The patients with an ID consult had a higher fungal burden but a lower 90-day mortality compared to patients without ID involvement (27% vs 45%, p<0.001), with an adjusted hazard ratio of not receiving an ID consult of 4.1 (95% CI: 2.2, 7.6). The ID consult group was more likely to receive an indicated lumbar puncture (86% vs 32%, p<0.001), and more likely to be treated with amphotericin B (AmB) (87% vs 24%, p<0.001) and flucytosine (5-FC) (57% vs 16%, p<0.001) when indicated. The duration of therapy with AmB (14 vs 11 days, p=0.05) and 5-FC (7.5 vs 1 days, p<0.001) was longer in the ID consult group. Conclusions Patients that received an ID consult were significantly less likely to die in the 90 days following diagnosis. Patients seen by ID physicians were more likely to be managed according to evidence based practice established by randomized controlled trials and published in IDSA guidelines. These data suggest that an ID consult should be an integral part of clinical care of patients with cryptococcosis.
Prevalence and Severity of Malocclusion in Adolescent Kuwaitis

Objectives: Our aim was to evaluate prevalence and severity of malocclusion in an adolescent Kuwaiti population. Subjects and Methods: Using a stratified cluster sampling method and excluding non-Kuwaitis, subjects with mesial migration and/or loss of first molars, and subjects with orthodontic treatment experience without availability of initial study models, we examined 1,299 Kuwaitis (674 boys and 625 girls) of mean age 13.2 ± 0.4 years in a regular well lit classroom. We scored molar and canine relationship, overjet, overbite, anterior and posterior cross bite as well as spacing and irregularity of the incisors using gloves, mirrors, rulers, and spatulas. Results: Fourteen, 15, and 71% met the criteria for almost ideal, mild, and moderate to severe malocclusion, respectively. Of the 86% with malocclusion, occurrence of class 1, half step class 2, full step class 2, half step class 3, and full step class 3 was 57.8, 24.9, 6.3, 8.8, and 2.2% for the first molars, and 36.1, 50.0, 6.2, 5.4, and 2.3% for the canines, respectively. Incisor malalignment was the most prevalent malocclusion trait (73.2%). Overjet ≧9.5 mm occurred in less than 1.5%, open bite in less than 3.5%, deep bite with gingival contact in less than 2.0%, complete posterior cross bite in less than 1.5%, and complete anterior crossbite in less than 2.0%. Median diastema was present in about 2/3 of the cases with maxillary anterior spacing as opposed to only about 1/3 of those with mandibular spacing. Conclusion: Our findings suggest that more than 70% of young adolescent Kuwaitis have moderate to severe malocclusion, with incisor malalignment as the most prevalent malocclusion trait.
Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.
The Contribution of Experimental in vivo Models to Understanding the Mechanisms of Adaptation to Mechanical Loading in Bone

Changing loading regimens by natural means such as exercise, with or without interference such as osteotomy, has provided useful information on the structure:function relationship in bone tissue. However, the greatest precision in defining those aspects of the overall strain environment that influence modeling and remodeling behavior has been achieved by relating quantified changes in bone architecture to quantified changes in bones’ strain environment produced by direct, controlled artificial bone loading. Jiri Hert introduced the technique of artificial loading of bones in vivo with external devices in the 1960s using an electromechanical device to load rabbit tibiae through transfixing stainless steel pins. Quantifying natural bone strains during locomotion by attaching electrical resistance strain gages to bone surfaces was introduced by Lanyon, also in the 1960s. These studies in a variety of bones in a number of species demonstrated remarkable uniformity in the peak strains and maximum strain rates experienced. Experiments combining strain gage instrumentation with artificial loading in sheep, pigs, roosters, turkeys, rats, and mice has yielded significant insight into the control of strain-related adaptive (re)modeling. This diversity of approach has been largely superseded by non-invasive transcutaneous loading in rats and mice, which is now the model of choice for many studies. Together such studies have demonstrated that over the physiological strain range, bone’s mechanically adaptive processes are responsive to dynamic but not static strains; the size and nature of the adaptive response controlling bone mass is linearly related to the peak loads encountered; the strain-related response is preferentially sensitive to high strain rates and unresponsive to static ones; is most responsive to unusual strain distributions; is maximized by remarkably few strain cycles, and that these are most effective when interrupted by short periods of rest between them.
In vitro and in vivo evaluation of ketotifen fumarate-loaded silicone hydrogel contact lenses for ocular drug delivery

The purpose of this work was to evaluate the usefulness of silicone hydrogel contact lenses loaded with ketotifen fumarate for ocular drug delivery. First, silicone contact lenses were prepared by photopolymerization of bitelechelic methacrylated polydimethylsiloxanes macromonomer, 3-methacryloxypropyltris(trimethylsiloxy)silane, and N,N-dimethylacrylamide using ethylene glycol dimethacrylate as a cross-linker and Darocur 1173 as an initiator followed by surface plasma treatment. Then, the silicone hydrogel matrices of the contact lenses were characterized by equilibrium swelling ratio (ESR), tensile tests, ion permeability, and surface contact angle. Finally, the contact lenses were loaded with ketotifen fumarate by pre-soaking in drug solution to evaluate drug loading capacity, in vitro and in vivo release behavior of the silicone contact lenses. The results showed that ESR and ion permeability increase, and the surface contact angle and tensile strength decreased with the increase of DMA component in the silicone hydrogel. The drug loading and in vitro releases were dependent on the hydrogel composition of hydrophilic/hydrophobic phase of the contact lenses. In rabbit eyes, the pre-soaked contact lenses sustained ketotifen fumarate release for more than 24 h, which leads to a more stable drug concentration and a longer mean retention time in tear fluid than that of eye drops of 0.05%.
On the role of abduction

The notion of explanation is basilar in many human behaviors and indeed in many elds (such as philosophy or psychology) there is a long tradition in the study of such a notion. In particular, reasoning towards explanation is a basic task in many of the problem solving activities investigated by the AI community. For example, it is the core of diagnostic problem solving (whose goal is to explain symptoms observed in a system with the presence of some faults) or of interpretation activities (e.g., image or story interpretation or plan recognition), and it is a basic component of machine learning (where the goal is to produce some theory that accounts for and generalizes some phenomena). Following a logicist tradition, many AI researchers working on explanation reduced such a notion to deduction: a phenomenon is explained when it can be deduced from a domain theory, possibly after some assumptions. Indeed, the interesting case is the one where the observed phenomenon does not follow from the original theory and some assumptions have to be made; in particular, one may either assume the truth of some facts mentioned in the theory or extend the theory itself. The term \abduction" has been often used to characterize the type of inference performed in the former case (while \induction" is closer to the latter case); as a consequence, the basic pattern of abduction can be seen as the ability of assuming a fact A in case A is a possible explanation for another fact B to be explained. From a logical point of view, this corresponds to the unsound inference concluding A from A! B and B. Abduction is thus a form of non-classical inference whose properties (e.g., non-monotonicity) are similar to those of other non-classical logics proposed and studied in the AI literature. Given such premises, one would expect that abduction played a central role in the logical approaches to AI. In fact, however, many researchers are quite di dent about such a form of reasoning and some criticisms have arisen in the
Molecular characterization and expression profiles of cyclin B 1 , B 2 and Cdc 2 kinase during oogenesis and spermatogenesis in rainbow trout ( Oncorhynchus mykiss )

The meiotic maturation of oocyte and spermatocyte in animals is controlled by the maturation promotion factor (MPF), a complex of Cdc2 and cyclin B proteins. To better understand the mechanism of oocyte and spermatocyte maturation in fish, the expression of cyclin B1 (CB1), B2 (CB2) and Cdc2 kinase during oogenesis and spermatogenesis in rainbow trout were examined at both the mRNA and protein levels. Quantitative real-time PCR analysis showed that the amount of CB1 and CB2 mRNA was greater at previtellogenesis and late vitellogenesis stages, but less at early vitellogenesis stage and during early embryogenesis. Cdc2 mRNA was continuously present throughout the processes of oogenesis and early embryogenesis except for a decline at early vitellogenesis. In situ hybridization analysis indicated that CB1, CB2 and Cdc2 transcripts were present in oocytes of different developmental stages as well as in all spermatogenic cells except for spermatogonia. Immunohistochemical analysis revealed that CB1 protein was absent in vitellogenic oocytes, but present in young previtellogenic and mature oocytes. In contrast, CB2 and Cdc2 proteins were present at all stages oocyte development. Similarly, CB2 and Cdc2 proteins were present throughout spermatogenesis, whereas CB1 protein was only detected in spermatogonia and spermatocytes, but not in spermatids. Thus, it appears that CB1, CB2 and Cdc2 transcripts have similar expression patterns during oogenesis and spermatogenesis, but CB1 protein varies in amount during these processes. ∗ Corresponding author. Tel. : +1 304 293 2631x4414; fax: +1 304 293 2232. E-mail address: jianbo.yao@mail.wvu. edu (J. Yao). 0378-4320/$ – see front matter © 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.anireprosci. 2007.03. 005 210 G. -F. Qiu et al. / Animal Reproduction Science 105 (2008) 209–225 These data suggest that CB1 may have a leading role in the regulation of meiotic maturation of oocytes and spermotocytes. © 2007 Elsevier B.V. All rights reserved.
Genetic, clinical and pharmacological determinants of out-of-hospital cardiac arrest: rationale and outline of the AmsteRdam Resuscitation Studies (ARREST) registry

Introduction Out-of-hospital cardiac arrest (OHCA) is a major public health problem. Recognising the complexity of the underlying causes of OHCA in the community, we aimed to establish the clinical, pharmacological, environmental and genetic factors and their interactions that may cause OHCA. Methods and analysis We set up a large-scale prospective community-based registry (AmsteRdam Resuscitation Studies, ARREST) in which we prospectively include all resuscitation attempts from OHCA in a large study region in the Netherlands in collaboration with Emergency Medical Services. Of all OHCA victims since June 2005, we prospectively collect medical history (through hospital and general practitioner), and current and previous medication use (through community pharmacy). In addition, we include DNA samples from OHCA victims with documented ventricular tachycardia/fibrillation during the resuscitation attempt since July 2007. Various study designs are employed to analyse the data of the ARREST registry, including case–control, cohort, case only and case-cross over designs. Ethics and dissemination We describe the rationale, outline and potential results of the ARREST registry. The design allows for a stable and reliable collection of multiple determinants of OHCA, while assuring that the patient, lay-caregiver or medical professional is not hindered in any way. Such comprehensive data collection is required to unravel the complex basis of OHCA. Results will be published in peer-reviewed journals and presented at relevant scientific symposia.
Blobby: how to guide a blind person

For the majority of blind people, walking in unknown places is a very difficult, or even impossible, task to perform, when without help. The adoption of the white cane is the main aid to a blind user's mobility. However, the major difficulties arise in the orientation task. The lack of reference points and the inability to access visual cues are its main causes. We aim to overcome this issue allowing users to walk through unknown places, by receiving a familiar and easily understandable feedback. Our preliminary contributions are in understanding, through user studies, how blind users explore an unknown place, their difficulties, capabilities and needs. We also analyzed how these users create their own mental maps, verbalize a route and communicate with each other. Structuring and generalizing this information, we were able to create a prototype that generates familiar and adequate instructions, behaving like a blind companion, one with similar capabilities that understands his "friend" and speaks the same language. We evaluated the system with the target population, validating our approach and orientation guidelines, while gathering overall user satisfaction.
The Capacity of Gaussian MIMO Channels Under Total and Per-Antenna Power Constraints

The capacity of a fixed Gaussian multiple-input multiple-output (MIMO) channel and the optimal transmission strategy under the total power (TP) constraint and full channel state information are well known. This problem remains open in the general case under individual per-antenna (PA) power constraints, while some special cases have been solved. These include a full-rank solution for the MIMO channel and a general solution for the multiple-input single-output (MISO) channel. In this paper, the fixed Gaussian MISO channel is considered and its capacity and optimal transmission strategies are determined in a closed form under the joint total and PA power constraints in the general case. In particular, the optimal strategy is hybrid and includes two parts: first is equal-gain transmission and second is maximum-ratio transmission, which are responsible for the PA and TP constraints, respectively. The optimal beamforming vector is given in a closed form and an accurate yet simple approximation to the capacity is proposed. Finally, the above results are extended to the MIMO case by establishing the ergodic capacity of fading MIMO channels under the joint power constraints when the fading distribution is right unitary-invariant (of which i.i.d. and semi-correlated Rayleigh fading are special cases). Unlike the fixed MISO case, the optimal signaling is shown to be isotropic in this case.
COLOR GLASS CONDENSATE IN BRANE MODELS OR DON'T ULTRA HIGH ENERGY COSMIC RAYS PROBE 1015eV SCALE?

In a previous work1 we have studied the propagation of relativistic particles in the bulk for some of the most popular brane models. Constraints have been put on the parameter space of these models by calculating the time delay due to propagation in the bulk of particles created during the interaction of Ultra High Energy Cosmic Rays (UHECRs) with protons in the terrestrial atmosphere. The question was, however, raised that probability of hard processes in which bulk modes can be produced is small and consequently, the tiny flux of UHECRs cannot constrain brane models. Here we use Color Glass Condensate (CGC) model to show that effects of extra dimensions are visible not only in hard processes when the incoming photon/parton hits a massive Kaluza–Klein mode but also through the modification of soft/semi-hard parton distribution. At classical level, for an observer in the CM frame of UHECR and atmospheric hadrons, color charge sources are contracted to a thin sheet with a width inversely proportional to th.
Determinants of youth participation in dry season vegetables cultivation in urban areas of Ondo State, Nigeria

The study investigate the determinants of youth participation in dry season vegetables cultivation in urban areas of Ondo state, Nigeria. Multistage sampling technique was used to select 120 respondents. Structured questionnaire were administered on respondents to elicit information on socio-economic/demographic characteristics and other variables. Descriptive statistics was employed to analyse the socio-economic/demographic characteristics of respondents, while logistic regression model was used to ascertain determinants of youth participation in dry season vegetables cultivation. Mean age of respondents was 24.7±3.4years, 65.5% were male, 58.6% were married, and 72.4% had formal education with 8.4±2.5years of experience. Major challenges facing youth in the study area were inadequate capital, lack of inputs and small farm size among others. The logistic regression analysis, revealed that; age, level of education, household size and access to credit, among others were the significant variables influencing youth participation in dry season vegetables cultivation at P≤0.05. Major constraints hindering youth in the study area were inadequate capital and farm land and poor inputs supply. Youth engagement in dry season vegetables cultivation has helped to provide employment/jobs, income, alleviate poverty, and arrest youth restiveness in the urban centres. It was recommended that access to credit and inputs supply should be made a necessity to youth.
CORRELATED MORPHOMETRIC AND BIOCHEMICAL STUDIES ON THE LIVER CELL

The basic morphological properties of liver cells are defined in the form of a morphometric model to permit integrated quantitative characterization of functionally important parameters. Stereologic methods which allow efficient and reliable quantitative evaluation of sectioned liver tissue are presented. Material, obtained by a rigorous three-stage sampling procedure from five normal rat livers, is systematically subjected to this analysis at four levels of magnification. This yields quantitative data which are expressed as "densities," i.e. content per 1 ml of tissue, as "specific dimensions" related to 100 g body weight, and as absolute dimensions per average "mononuclear" hepatocyte. Base line data relating to the normal rat liver are presented for the entire spectrum of parameters. As examples, 1 ml of liver tissue contains 169 x 106 hepatocyte nuclei, some 90 x 106 nuclei of other cells, and 280 x 109 mitochondria. Hepatocyte cytoplasm accounts for 77% of liver volume, and the mitochondria for 18%. The surface area of endoplasmic reticulum membranes in 1 ml of liver tissue measures 11 m2 of which are ⅔ of the rough form carrying some 2 x 1013 ribosomes. The surface area of mitochondrial cristae in the unit volume is estimated at 6 m2. The validity and applicability of the method are discussed, and the data are compared with available information from other studies.
The 19-kDa Mycobacterium tuberculosis Protein Induces Macrophage Apoptosis Through Toll-Like Receptor-21

Macrophages infected with Mycobacterium tuberculosis undergo increased rates of apoptosis. Important objectives are to define the microbial factors that cause apoptosis, the mechanisms involved and the impact on infection. The 19-kDa M. tuberculosis glycolipoprotein (p19) is both cell wall-associated and secreted and is a candidate virulence factor. We investigated the potential of recombinant, His-tagged p19 lacking the secretion/acylation signal to induce macrophage apoptosis. The TUNEL assay and annexin V binding to membrane phosphatidylserine were used to measure apoptosis. The results show that p19 does act to induce apoptosis in differentiated THP-1 cells and monocyte-derived macrophages and that this effect is both dose- and time-dependent. Furthermore, this effect of p19 is Toll-like receptor (TLR)-2-mediated because preincubation of either THP-1 cells or TLR-2-expressing CHO cells with anti-TLR-2 mAb inhibited apoptosis induced by p19. Apoptosis of macrophages in response to p19 was found to be caspase-8 dependent and caspase-9 independent consistent with a transmembrane pathway signaling cell death through TLR-2. The viability of M. tuberculosis in cells undergoing apoptosis induced by p19 was significantly reduced suggesting the possibility that this may favor containment of infection. Although native p19 is a mycobacterial glycolipoprotein, based upon the use of recombinant p19 where the acylation signal had been removed, we conclude that it is the polypeptide component of p19 that is responsible for signaling through TLR-2 and that the lipid moiety is not required.