Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of Bias in Different Cosmological Models

We study the evolution of the halo-halo correlation function and small-scale (≈0.2-7 h-1 Mpc) bias in four cosmological models (ΛCDM, OCDM, τCDM, and SCDM) using very high resolution n-body simulations with a dynamical range of ~10,000-32,000 (force resolution of ≈2-4 h-1 kpc and particle mass of ≈109 h-1 M☉). The high force and mass resolution allows dark matter halos to survive in the tidal fields of high-density regions and thus prevents the ambiguities related with the "overmerging problem. " This allows us to estimate for the first time the evolution of the correlation function and bias at small (down to ~100 h-1 kpc) scales. We find that at all epochs the two-point correlation function of galaxy-size halos ξhh is well approximated by a power law with slope ≈1.6-1.8. The difference between the shape of ξhh and the shape of the correlation function of matter results in the scale-dependent bias at scales ≲7 h-1 Mpc, which we find to be a generic prediction of the hierarchical models, independent of the epoch and of the model details. The bias evolves rapidly from a high value of ~2-5 at z ~ 3-7 to the antibias of b ~ 0.5-1 at small ≲5 h-1 Mpc scales at z = 0. Another generic prediction is that the comoving amplitude of the correlation function for halos above a certain mass evolves nonmonotonically: it decreases from an initially high value at z ~ 3-7, and very slowly increases at z ≲ 1. We find that our results agree well with existing clustering data at different redshifts, indicating the general success of the hierarchical models of structure formation in which galaxies form inside the host DM halos. Particularly, we find an excellent agreement in both slope and the amplitude between ξhh(z = 0) in our ΛCDM60 simulation and the galaxy correlation function measured using the Automatic Plate Measuring Facility galaxy survey. At high redshifts, the observed clustering of the Lyman-break galaxies is also well reproduced by the models. We find good agreement at z ≳ 2 between our results and predictions of the analytical models of bias evolution. This indicates that we have a solid understanding of the nature of the bias and of the processes that drive its evolution at these epochs. We argue, however, that at lower redshifts the evolution of the bias is driven by dynamical processes inside the nonlinear high-density regions such as galaxy clusters and groups. These processes do not depend on cosmology and tend to erase the differences in clustering properties of halos that exist between cosmological models at high z.
Induction of rapid and highly efficient expression of the human ND4 complex I subunit in the mouse visual system by self-complementary adeno-associated virus.

OBJECTIVE To demonstrate the high efficiency and rapidity of allotopic expression of a normal human ND4 subunit of complex I in the vertebrate retina using a self-complementary adeno-associated virus (scAAV) vector for ocular gene delivery to treat acute visual loss in Leber hereditary optic neuropathy (LHON). METHODS The nuclear-encoded human ND4 subunit fused to the P1 isoform of subunit C of adenosine triphosphate synthase (ATPc) mitochondrial targeting sequence and FLAG epitope was packaged in scAAV2 capsids or single-stranded (ss) AAV2 capsids. These constructs were injected into the vitreous cavities of mice. The contralateral eyes were injected with scAAV-green fluorescent protein (GFP). One week later, pattern electroretinograms and gene expression of the human ND4 subunit and GFP were evaluated. Quantitative analysis of ND4FLAG-injected eyes was assessed relative to Thy1.2-labeled retinal ganglion cells (RGCs). RESULTS Pattern electroretinogram amplitudes remained normal in eyes inoculated with scAAV-ND4FLAG, ssAAV-ND4FLAG, and GFP. Confocal microscopy revealed the typical perinuclear mitochondrial expression of scAAV-ND4FLAG in almost the entire retinal flat mount. In contrast, scAAV-GFP expression was cytoplasmic and nuclear. Relative to Thy1.2-positive RGCs, quantification of scAAV-ND4FLAG-positive RGCs was 91% and that of ssAAV-ND4FLAG-positive RGCs was 51%. CONCLUSION Treatment of acute visual loss due to LHON may be possible with a normal human ND4 subunit gene of complex I, mutated in most cases of LHON, when delivered by an scAAV vector. Clinical Relevance Unlike most retinal degenerations that result in slowly progressive loss of vision over many years, LHON due to mutated mitochondrial DNA results in apoplectic, bilateral severe and usually irreversible visual loss. For rescue of acute visual loss in LHON, a highly efficient and rapid gene expression system is required.
Uridine diphosphate glucose pyrophosphorylase of Acanthamoeba castellanii. Purification, kinetic, and developmental studies.

Abstract When cells of Acanthamoeba castellanii (Neff) are placed on a salts medium the amoebas encyst with the formation of a cellulose-containing cyst wall and an in vitro system synthesizing cellulose from UDP-glucose becomes detectable after about 12 hours of encystment. In the present study cellular levels of UDP-glucose were observed to increase 5-fold within 5 hours of the induction of encystment and to remain at elevated levels for 5 to 10 hours, apparently making UDP-glucose available to the cells at the time of cellulose synthesis. The increased level of UDP-glucose during encystment is not the reflection of an increase in uridine diphosphate glucose pyrophosphorylase activity detectable in vitro. The specific activity and the activity per cell were examined as a function of development in cell extracts. The specific activity was constant for the first 20 hours of encystment while the activity per cell decreased almost from the beginning of encystment. The uridine diphosphate glucose pyrophosphorylase (EC 2.7.7.9) from trophozoites was purified to homogeneity as determined by polyacrylamide gel electrophoresis. The purified enzyme (final specific activity 15,833 units per mg) was highly specific for both UTP and UDP-glucose. The divalent cation requirement was most readily satisfied by magnesium and the pH optimum was 8 to 9 in the direction of UDP-glucose synthesis and 7.5 to 7.6 in the direction of pyrophosphorolysis. The enzyme was characterized kinetically as having an ordered mechanism of catalysis. Pyrophosphorylase was subject to product inhibition by UTP and pyrophosphate. The following Km values were obtained: UTP, 5.8 x 10-5 m; glucose 1-phosphate, 1.4 x 10-4 m; UDP-glucose, 5.0 x 10-5 m; pyrophosphate, 2.4 x 10-3 m.
The Effects of Activity and Gain Based Virtual Material on Student's Success, Permanency and Attitudes towards Science Lesson.

The main objective of this study is to research the effects of a student gains and activity based virtual material on students’ success, permanence and attitudes towards science lesson, developed for science and technology lesson 6th grade “Systems in our body” unit. The study, which had a quasi-experimental design, was conducted with the participation of a total of 70 6th graders in a primary school. Before the study, a virtual material was developed by research which consisted of interactive activities for each of students’ gains of the unit. In the experimental group, the virtual material was used by the teacher while teaching the unit. The Unit was treated in the usual way in the control group during the study. Achievement test, permanence test and science and technology lesson attitude scales were used as data collection tools and they were conducted on both groups as pre-test and post-test. SPSS 17 package program was used in the analysis of the data. As a conclusion, a significant difference in favor of the experimental group was found in students’ achievement. But, it was not seen that virtual material based on activity and gain affected permanency in a positive way. Also, no statistically significant difference was found between groups as to students’ achievement. In addition, when the attitudes of experimental and control group students towards the lesson after the study were examined, no statistically significant difference was found in post-test and permanency tests.
Estrogen Replacement Therapy Among Post-menopausal Women and Its Effects on Signs and Symptoms of Temporomandibular Disorders

Abstract The prevalence of temporomandibular disorders (TMD) is about two to five times higher in females than in males. Data for the higher prevalence of TMD in women and prevalence rates peak during the reproductive years and decrease after menopause. This indicated that female sex hormones may play a role in the etiology or maintenance of TMD. The aim of this study was to investigate the relationship between postmenopausal hormone use and TMD in Turkish postmenopausal women. One hundred-eighty (180), postmenopausal women, aged 42-72 years, were examined both clinically and by questionnaire with regard to the signs and symptoms of temporomandibular disorders, general health status and use of postmenopausal hormone replacement therapy in the preceding year. Ninety-one (91) postmenopausal women (50.6%) were on hormone replacement therapy (HRT). The remaining 89 (49.4%) postmenopausal women were not on hormone replacement therapy. There was no significant difference found in the signs and symptoms of TMD between postmenopausal women using hormone therapy and those not using postmenopausal hormones. There was no association between the use of postmenopausal hormones and the signs and symptoms of TMD in this study.
Hypertonic saline attenuation of the neutrophil cytotoxic response is reversed upon restoration of normotonicity and reestablished by repeated hypertonic challenge.

BACKGROUND Hypertonic saline (HTS) resuscitation, in addition to enhancing hemodynamic recovery, modulates postinjury hyperinflammation in the critically injured. The polymorphonuclear neutrophil (PMN) cytotoxic response, a key element in the pathogenesis of postinjury organ dysfunction, is attenuated under hypertonic conditions. Although plasma Na(+) rises to 180 mmol/L after HTS infusion, baseline levels are reestablished within 24 hours. We hypothesized that HTS attenuation of the PMN cytotoxic response (beta2-integrin expression, elastase release, and O2- production) is reversed upon return to normotonicity, but can be reestablished by repeated HTS challenge. METHODS Isolated human PMNs were incubated in HTS (Na(+) = 180 mmol/L) for 5 minutes at 37 degrees C then returned to normotonicity by centrifugation and resuspension in isotonic buffer. Stimulated (PAF) beta2-integrin expression was measured by flow cytometry. Stimulated (PAF/fMLP) elastase release and O2- production were measured by cleavage of N-methoxysuccinyl-Ala-Ala-Pro-Val p-nitroanilide and reduction of cytochrome c (Cyt c). Protein tyrosine phosphorylation in PMN cell lysates was assessed by Western blot. RESULTS Clinically relevant levels of HTS induced tyrosine phosphorylation in resting PMNs and attenuated cytotoxic responses. Reestablishment of normotonicity returned these functions to baseline. A repeated HTS challenge after restoration of normotonicity also induced tyrosine phosphorylation and suppressed the cytotoxic response. CONCLUSIONS HTS attenuation of the PMN cytotoxic response is reversible but can be reestablished by repeated HTS treatment. This phenomenon may provide the unique opportunity to selectively and temporarily decrease the postinjury inflammatory response when patients are at greatest risk for PMN-mediated tissue damage.
Effects of storage at -20 degrees C on ischaemia-modified albumin results.

BACKGROUND Ischaemia-modified albumin (IMA) is being studied as a new marker for reversible ischaemia in patients presenting with possible cardiac chest pain. The conditions under which samples are stored prior to analysis may be critical in influencing the analytical result and hence the cut-off used in any particular study. METHODS Sixty-eight samples taken during a study assessing the performance of IMA for risk stratification in patients presenting with possible cardiac chest pain were analysed both within 2.5 h of collection and after periods of storage at -20 degrees C. RESULTS Samples stored at -20 degrees C yielded IMA values on average 3 units higher than those analysed within 2.5 h (mean 90.5 vs. 87.5; P < 0.00001). A Bland-Altman plot showed that the difference was not concentration dependent. CONCLUSIONS These results indicate that decision cut-offs will be influenced by conditions of sample storage prior to IMA analysis, and that these should be stated in detail for each study.
Population pharmacokinetics of mavacoxib in osteoarthritic dogs.

Mavacoxib (Trocoxil™) is an oral long-acting COX-2 inhibitor approved for the treatment of osteoarthritis in dogs. Two field trials were conducted in client-owned dogs suffering from osteoarthritis, with dosages of 4 mg/kg body weight (BW) (Study 1) or 2 mg/kg BW (Study 2). Mavacoxib plasma concentrations were determined from trough blood samples and from blood samples collected at 4-10 months after the last dose. A one-compartment linear model was fitted to the concentration data (1317 concentration records from 286 patients), and parameters for oral clearance (Cl/F), apparent volume of distribution (V(d) /F) and their between-subject variabilities (BSV) were estimated. Covariates were included in the model based on the outcomes of stepwise regression procedures. In the final model, the typical value of Cl/F was a function of BW, age and breed. German shepherds and Labrador retrievers were found to have 31% higher values of Cl/F than patients from different breeds with similar ages and BWs. The typical value of V(d) /F was found to be dependent only on BW. The two field studies appeared to differ similarly with respect to Cl/F and V(d) /F. The explanation for this difference is not known, but the difference was accounted for in the final model as a 23.9% lower bioavailability in Study 2. Mavacoxib exhibited relatively broad BSV in Cl/F and V(d) /F, with coefficients of variation of 47% and 19%, respectively. The typical value for mavacoxib's terminal elimination plasma half-life (t(1/2) ) was 44 days, but a minority of patients (approximately 5%) had empirical Bayes estimates of t(1/2) exceeding 80 days. Simulations with the model indicated that the majority of patients treated with mavacoxib 2 mg/kg will maintain trough plasma mavacoxib concentrations associated with efficacy. Results of the population pharmacokinetic analysis helped to reduce the dose from 4 to 2 mg/kg and thus increased the therapeutic index for this molecule.
NICE guideline for the management of head injury: an audit demonstrating its impact on a district general hospital, with a cost analysis for England and Wales

Objectives: To answer concerns related to implementation of the National Institute for Clinical Excellence (NICE) guideline on the management of head injury by determining the impact on the workload of a district general hospital. Increased computed tomography (CT) was of particular concern (cost, radiation risk, and delivery constraints). Method: Retrospective audit of all patients attending the hospital’s emergency department with a head injury over a three month period. Any reattendees for the same head injury episode were excluded but the need for CT was recorded. Case notes and electronic records were reviewed to determine whether the CT head or skull radiograph (SXR) was indicated in line with the NICE guideline. The workload was compared with an identical audit performed before the implementation of the NICE guideline. Results: Of 17 472 patients attending the ED in 2004, 472 had a head injury. CT scan was indicated in 36, a significant increase from 2003 (p<0.001). No SXR was indicated but two were performed, a significant decrease (p<0.001). The admission rate was unaltered. The positive predictive value of NICE was 17.1% compared with 25% (p = not significant) for the authors’ pre-NICE departmental guideline. Conclusions: This department has seen an increase in CT head requests since the implementation of the NICE guideline. This costs an extra £15 000 per 100 head injuries annually for this department, with an estimated £51.7 million burden for England and Wales. Further evaluation is required as there were only nine brain injuries in this audit population.
Cytochrome P450 3A4 and P‐glycoprotein Activity and Assimilation of Tacrolimus in Transplant Patients with Persistent Diarrhea

Renal transplant recipients suffering from persistent diarrhea have been repeatedly reported to have increased tacrolimus (Tac) trough levels. This study aimed to explore this phenomenon in detail in 15 renal transplant recipients with diarrhea, whose immunosuppression consisted of corticosteroids, mofetil mycophenolate and Tac. Both hepatic and intestinal CYP3A4 and PGP activity, important determinants of Tac bioavailability, were assessed, together with global CYP activity and investigations for gastrointestinal infection, function and morphology. Global CYP, CYP3A4, PGP and trough/dose levels of Tac were compared with diarrhea‐free controls. In addition, a pharmacokinetic study of Tac was performed in 11 patients affected by diarrhea versus 9 controls. As expected, diarrhea was associated with increased Tac trough levels. An even stronger, significant increase of dose‐normalized Tac levels was observed between 90 and 360 min after Tac intake. Time to peak concentration and drug half‐life, however, were not altered. In addition, a concomitant decrease (±50%) of intestinal PGP activity was noticed in patients with diarrhea. For global CYP, CYP3A4 and hepatic PGP activity no such differences were noted. This pattern was not influenced by the specific cause of diarrhea. These data strongly suggest that persistent diarrhea is associated with an increased oral bioavailability of Tac.
Uncovering a Novel Mechanism for Gene Expression Regulation with a Random Forest Classifier

Trypanosoma brucei is a devastating parasite which infects tens of thousands of people in sub-Saharan Africa, causing a deadly disease known as African sleeping sickness [1]. The parasite is transmitted from human to human via an insect vector known as the tsetse fly, which feeds on human blood [1]. T. brucei possesses a highly unusual genome. Unlike most organisms in its phylogenetic domain, this single-celled protozoan and several other closely related species lack a vital biological mechanism for regulating the expression of their genes [2]. Scientific evidence indicates that the parasite does indeed feature different levels of gene expression in its two host environments (the human bloodstream and the tsetse fly midgut) [2]. This suggests that T. brucei exploits a different mechanism than most other organisms for regulating the expression of its genes [2]. This study will explore the hypothesis that the parasite exploits the change in temperature across its two host environments to induce changes in RNA structure that affect gene expression. Using a random forest classifier, we demonstrate that nine variables describing change in RNA structure for T. brucei genes across host temperatures may be successfully utilized to classify genes according to their expression in the parasite’s two hosts. A bootstrapping procedure is implemented to verify that the classifier performs significantly better than chance.
Conventional DMARD therapy (methotrexate‐sulphasalazine) may decrease the requirement of biologics in routine practice of ankylosing spondylitis patients: A real‐life experience

The effect of disease‐modifying antirheumatic drugs (DMARDs) in ankylosing spondylitis (AS) is still controversial. We aimed to evaluate the efficacy of sulphasalazine (SSZ) mono‐ or combination therapy with methotrexate (MTX) in AS patients naive to anti‐tumor necrosis factor alpha (TNFα) agents.
The impact of knowledge repositories on power and control in the workplace

Knowledge management systems designed to facilitate the storage and distribution of codified knowledge affect the distribution of power within organizations. Drawing on the literature that describes the impact of information technology on power and control, this article proposes two principal outcomes of the implementation and use of such knowledge repositories. The use of knowledge repositories by employees who are net re‐users of knowledge‐based work products is expected to increase the extent to which these employees are interchangeable while reducing the level of skill they need to carry out their work. For employees who are net contributors to knowledge‐based work products, the use of knowledge repositories produces the opposite effect. When managers choose to capitalize on these effects to increase their control, employees in the former group may find their power position eroded over time.
Oil rents and fiscal balance in oil dependent economies: do fiscal rules matter?

In this paper, we utilize a panel of oil dependent economies from 2000 to 2015 and attempt to empirically examine the relationship between crude oil rents and fiscal balance, while controlling for other covariates. Our strategy is to highlight the importance of fiscal rules by using an instrumental variable approach based on Dynamic Panel estimators [the General Method of Moment (GMM)]. This is used in comparison with estimations from pooled OLS, LSDV fixed effects, and the IV/2SLS techniques (using each country`s share of world output as instrument). Our pre-estimation diagnostics showed that the GMM approach might not be applicable to the small sample, and we suspected that the IV/2SLS method might also be weak in testing our hypothesis for the oil dependent economies; therefore we maintained the LSDV Fixed effects estimations. Our estimation results shows that in countries with fiscal rules, there is insignificant reaction of fiscal balance to changes in oil rents shocks, and the impact is weak. We find also that welfare spending, which was captured by the real GDP per capita, affects fiscal balance, and so does the budgetary variable, i.e. debt-to-GDP ratio, and the ability of the government to curb corruption and mismanagement of funds, which is politically motivated.
Influence of some endocrine glands, hormones and blinding on the histology and porphyrins of the Harderian glands of golden hamsters.

Harderian glands of female or castrated male hamsters contained scattered luminal pigment deposits and a single cell type. Two cell types were found in the glands from intact males. Glands from both male and female animals showed abundant cytoplasmic lipids. Pigment formation appeared to be endogenous and in some cases occurred by extrusion of cells from alveolar walls and their subsequent transformation. Holocrine secretion was demonstrable. Porphyrin concentrations in the glands from females were increased three weeks after bilateral blinding and decreased following hypophysectomy, ablation of one Harderian gland, unilateral blinding, treatment with thiourea or exposure to an environmental temperature of 8°C. Ovariectomy or ovariectomy plus treatment with 17-α-estradiol for three weeks had no effect on the Harderian glands nor did pinealectomy. Porphyrin concentrations in the glands from male hamsters were extremely low. Castration increased these concentrations over 100-fold and modified the morphology toward that of the female while testosterone proprionate treatment prevented these changes. Administration of H3-thymidine and subsequent radioautography revealed a peak in mitotic activity between 9:30 PM and 12:30 AM at the end of the light period or the beginning of the dark period. Longterm blinded or blinded, castrated males had Harderian glands which were microscopically “lacelike” due to intense steatogenesis.