Miracle-dz/UniFAR-FTUs huggingface dataset:
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5′ and 3′ half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3–6 days before symptom onset and 14–17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized.
Findings from Structural MR Imaging in Military Traumatic Brain Injury.

PURPOSE To describe the initial neuroradiology findings in a cohort of military service members with primarily chronic mild traumatic brain injury (TBI) from blast by using an integrated magnetic resonance (MR) imaging protocol. MATERIALS AND METHODS This study was approved by the Walter Reed National Military Medical Center institutional review board and is compliant with HIPAA guidelines. All participants were military service members or dependents recruited between August 2009 and August 2014. There were 834 participants with a history of TBI and 42 participants in a control group without TBI (not explicitly age- and sex-matched). MR examinations were performed at 3 T primarily with three-dimensional volume imaging at smaller than 1 mm(3) voxels for the structural portion of the examination. The structural portion of this examination, including T1-weighted, T2-weighted, before and after contrast agent administrtion T2 fluid attenuation inversion recovery, and susceptibility-weighted images, was evaluated by neuroradiologists by using a modified version of the neuroradiology TBI common data elements (CDEs). Incident odds ratios (ORs) between the TBI participants and a comparison group without TBI were calculated. RESULTS The 834 participants were diagnosed with predominantly chronic (mean, 1381 days; median, 888 days after injury) and mild (92% [768 of 834]) TBI. Of these participants, 84.2% (688 of 817) reported one or more blast-related incident and 63.0% (515 of 817) reported loss of consciousness at the time of injury. The presence of white matter T2-weighted hyperintense areas was the most common pathologic finding, observed in 51.8% (432 of 834; OR, 1.75) of TBI participants. Cerebral microhemorrhages were observed in a small percentage of participants (7.2% [60 of 834]; OR, 6.64) and showed increased incidence with TBI severity (P < .001, moderate and severe vs mild). T2-weighted hyperintense areas and microhemorrhages did not collocate by visual inspection. Pituitary abnormalities were identified in a large proportion (29.0% [242 of 834]; OR, 16.8) of TBI participants. CONCLUSION Blast-related injury and loss of consciousness is common in military TBI. Structural MR imaging demonstrates a high incidence of white matter T2-weighted hyperintense areas and pituitary abnormalities, with a low incidence of microhemorrhage in the chronic phase.
PPARγ Gene Transfer Sustains Apoptosis, Inhibits Vascular Smooth Muscle Cell Proliferation, and Reduces Neointima Formation After Balloon Injury in Rats

Objective—There is still debate as to whether antiatherosclerotic effect of PPARγ ligands is dependant on PPARγ gene itself or some other pathway. Methods and Results—To investigate the effect of PPARγ gene modulation on neointima formation after balloon injury, we delivered adenoviral vectors expressing the wild-type (WT) dominant negative (DN) PPARγ, or a control gene (β-galactosidase [BG]) into carotid artery after balloon injury in rosiglitazone (a PPARγ ligand)-treated (R+) (3 mg/kg/d) and nontreated (R−) rats. Two weeks after gene delivery, in both R+ and R− animals, the PPARγ-WT gene transfer showed a significantly lower intima-media ratio (IMR) than control group. Moreover, the delivery of a PPARγ-DN form showed the highest IMR (in R+WT, 0.51±0.15; R+BG, 0.89±0.14; R+DN, 1.20±0.18, P<0.05 and in R−WT, 0.91±0.21; R−BG, 1.44±0.23; R−DN, 1.74±0.29, P<0.05). Proliferation and migration showed same result pattern as IMR. In addition, apoptotic indices were significantly higher in the PPARγ-WT gene transferred group than in the PPARγ-DN group. Conclusions—In vivo transfer of the PPARγ-WT gene was found to inhibit smooth muscle proliferation, sustain apoptosis, and reduce neointima formation after balloon injury irrespective of rosiglitazone treatment. These results indicate that PPARγ overexpression itself has a protective role against restenosis after balloon injury.
A System Dynamics Tool for Higher Education Funding and Quality Policy Analysis

Conceptually, the level of funding of higher education activities is directly proportional to its strategic directions/implementations and hence quality. In developing countries, these dependencies are far from straightforward due to ad-hoc reactions to reduced funding. This paper contributes to the development of tools for this management challenge. We investigate the dynamics of higher education funding and ensuing impact on part-time teaching, staff to student ratios, staff development, research productivity, and hence the perceived quality, using a system dynamics simulation model. The model developed is based on higher education literature in the developing world in general and Uganda in particular. We use the resulting model to review policies on funding and quality in higher education, and ultimately envisage that the model can easily be adapted to higher education in other environments.
The National Diabetes Register in Sweden: an implementation of the St. Vincent Declaration for Quality Improvement in Diabetes Care.

OBJECTIVE To monitor glycemic control, treatable risk factors, and treatment profile for quality assessment of diabetes care on a national scale. RESEARCH DESIGN AND METHODS Four samples of 23,546, 32,903, 30,311, and 29,769 patients with diabetes (1996-1999) were studied based on a repeated national screening and quality assessment of diabetes care by the National Diabetes Register, Sweden, with participation of both hospitals and primary health care. Clinical characteristics included were age, sex, diabetes duration and treatment, glycemic control (HbA(1c)), office blood pressure (BP), BMI, smoking habits, and use of lipid-lowering drugs in patients with type 1 or type 2 diabetes. RESULTS Favorable decreases of mean HbA(1c) and BP values were registered during the 4-year study period for both type 1 (HbA(1c) 7.5-7.3% and BP 130/75-130/74 mmHg) and type 2 diabetic patients (HbA(1c) 7.0-6.7% and BP 151/82-147/80 mmHg). Treatment aims of HbA(1c) and BP levels were also achieved in increasing proportions for type 1 (HbA(1c) <7.5%: 50-58% and BP </=140/85 mmHg: 77-79%), and type 2 diabetic patients (HbA(1c) <7.5%: 66-73% and BP </=140/85 mmHg: 32-42%). The use of lipid-lowering drugs increased for type 1 (4-11%) and type 2 diabetic patients (10-22%). In type 2 diabetic patients, treatment with oral agents alone decreased, but combination therapy (insulin and oral agents) increased during the study period. Mean BMI increased during 1996-1999 in type 2 diabetic patients. High HbA(1c) and BP values in 1999 were predicted by high BMI values 1996 and by high increase of BMI during the period, independent of diabetes duration, age, and sex. CONCLUSIONS Decreasing mean HbA(1c) and BP levels and the wider use of lipid-lowering drugs during the late 1990s in patients with diabetes in a national sample from Sweden should translate into clinical benefits regarding micro- and macrovascular complications as well as diabetes-related mortality.
Significance of Image Guidance to Clinical Outcomes for Localized Prostate Cancer

Purpose. To compare toxicity profiles and biochemical tumor control outcomes between patients treated with image-guided intensity-modulated radiotherapy (IG-IMRT) and non-IGRT intensity-modulated radiotherapy (IMRT) for clinically localized prostate cancer. Materials and Methods. Between 2009 and 2012, 65 patients with localized prostate cancer were treated with IG-IMRT. This group of patients was retrospectively compared with a similar cohort of 62 patients who were treated between 2004 and 2009 with IMRT to the same dose without image guidance. Results. The median follow-up time was 4.8 years. The rectal volume receiving ≥40 and ≥70 Gy was significantly lower in the IG-IMRT group. Grade 2 and higher acute and late GI and GU toxicity rates were lower in IG-IMRT group, but there was no statistical difference. No significant improvement in biochemical control at 5 years was observed in two groups. In a Cox regression analysis identifying predictors for PSA relapse-free survival, only preradiotherapy PSA was significantly associated with biochemical control; IG-IMRT was not a statistically significant indicator. Conclusions. The use of image guidance in the radiation of prostate cancer at our institute did not show significant reduction in the rates of GI and GU toxicity and did not improve the biochemical control compared with IMRT.
LY294002 and Metformin Cooperatively Enhance the Inhibition of Growth and the Induction of Apoptosis of Ovarian Cancer Cells

Background The phosphoinositide 3 kinase (PI3K)/v-akt murine thymoma viral oncogene homolog (AKT)/mammalian target of rapamycin (mTOR) pathway is frequently aberrantly activated in ovarian cancer and confers the chemoresistant phenotype of ovarian cancer cells. LY294002 (PI3K inhibitor) and metformin (5′-adenosine monophosphate [AMP]-activated protein kinase [AMPK] activator) are 2 drugs that were known to inhibit mTOR expression through the AKT-dependent and AKT-independent pathways, respectively. In this study, we explored the effectiveness of LY294002 and metformin in combination on inhibition of ovarian cancer cell growth. Methods Western blotting was used to detect the changes of PI3K/AKT/mTOR and AMPK/acetyl-CoA carboxylase (ACC) signaling activities, cell cycle control, and apoptosis. Cell growth was evaluated by cell proliferation, colony formation, and soft agar assays. Flow cytometry was used to study cell cycle distribution and cell death upon drug treatment. Results Our study showed that LY294002 and metformin in combination could simultaneously enhance the repression of the PI3K/AKT/mTOR pathway and the activation of the AMPK/ACC pathway. The downstream target of AKT and AMPK, mTOR, was cooperatively repressed when the drugs were used together. The cell cycle regulatory factors, p53, p27, and p21, were up-regulated. On the other hand, caspase 3 and poly (ADP-ribose) polymerase activities involved in apoptosis were also activated. Cell growth assays indicated that LY294002 and metformin could effectively inhibit ovarian cancer cell growth. Flow cytometry analysis showed that the treatment of the 2 drugs mentioned above induced cell cycle arrest at G1 phase and increased sub-G1 apoptotic cells. Conclusion The combinational use of LY294002 and metformin can enhance inhibition of the growth and induction of the apoptosis of ovarian cancer cells. Our results may provide significant insight into the future therapeutic regimens in ovarian cancer.
Strategies for Pandemic and Seasonal Influenza Vaccination of Schoolchildren in the United States

Vaccinating school-aged children against influenza can reduce age-specific and population-level illness attack rates. Using a stochastic simulation model of influenza transmission, the authors assessed strategies for vaccinating children in the United States, varying the vaccine type, coverage level, and reproductive number R (average number of secondary cases produced by a typical primary case). Results indicated that vaccinating children can substantially reduce population-level illness attack rates over a wide range of scenarios. The greatest absolute reduction in influenza illness cases per season occurred at R values ranging from 1.2 to 1.6 for a given vaccine coverage level. The indirect, total, and overall effects of vaccinating children were strong when transmission intensity was low to intermediate. The indirect effects declined rapidly as transmission intensity increased. In a mild influenza season (R = 1.1), approximately 19 million influenza cases could be prevented by vaccinating 70% of children. At most, nearly 100 million cases of influenza illness could be prevented, depending on the proportion of children vaccinated and the transmission intensity. Given the current worldwide threat of novel influenza A (H1N1), with an estimated R of 1.4–1.6, health officials should consider strategies for vaccinating children against novel influenza A (H1N1) as well as seasonal influenza.
White Matter Involvement in Idiopathic Parkinson Disease: A Diffusion Tensor Imaging Study

BACKGROUND AND PURPOSE: Diffusion tensor imaging (DTI) offers a unique window on the connectivity changes, extending beyond the basal ganglia, which accompany the cognitive symptoms of Parkinson disease (PD). The primary purpose of this study was to assess the microstructural damage to cerebral white matter occurring in idiopathic PD. MATERIALS AND METHODS: Our sample included patients with PD without dementia (n = 10; Hoehn and Yahr stages I and II; Unified Parkinson Disease Rating Scale, 20.5 ± 8.3; and Mini-Mental State Examination, 28.3 ± 1.5) and age-matched healthy control subjects (n = 10). DTI was performed on a 1.5T scanner, and mean diffusivity (MD) and fractional anisotropy (FA) maps were obtained. Regions of interest (ROIs) were drawn on the major fiber bundles as well as on gray matter nuclei. RESULTS: In patients, the MD was increased at borderline significance in the substantia nigra but was unaltered in the thalamus, globus pallidus, putamen, and in the head of the caudate nucleus. The FA and MD were unaltered in the corticospinal tract in the midbrain and at the level of the internal capsule, and in the splenium of the corpus callosum. By contrast, the MD was increased and the FA was decreased in the genu of the corpus callosum and in the superior longitudinal fasciculus; in the cingulum, only the MD was altered. The observed changes were not significantly lateralized. CONCLUSIONS: Widespread microstructural damage to frontal and parietal white matter occurs already in the early stages of PD.
Diabetic neuropathy

The diabetic polyneuropathy (DN) is a common disorder with diverse clinical presentations depending on the type and duration of diabetes, number of nerve fibers affected and its glycemic control. They progress in length-dependent pattern causing severe sensory-motor deficit, more common in distal lower limbs than in upper limbs. In addition, small fiber polyneuropathy has been identified in vast majority of patients affecting sensory and autonomic system in distal limbs. Excruciating pain, trophic changes in the feet, abnormal sweating and numbness are the main manifestations of small fiber DN. Occasionally diabetic neuropathy can present with focal and multifocal neuropathies of cranial, truncal and peripheral nerves among patients with long standing diabetes and age over 50. The length dependent DN hardly improves over period of time when compared to focal or multifocal neuropathy which is usually self-limiting after a course of few relapses. Therefore, adequate attention should be paid on early clinical diagnosis, identifying sub types and complications to tailor the appropriate treatment or to initiate preventive measures to avoid the devastating consequences of DN.
Bi-frontal transcranial alternating current stimulation in the ripple range reduced overnight forgetting

High frequency oscillations in the hippocampal structures recorded during sleep have been proved to be essential for long-term episodic memory consolidation in both animals and in humans. The aim of this study was to test if transcranial Alternating Current Stimulation (tACS) of the dorsolateral prefrontal cortex (DLPFC) in the hippocampal ripple range, applied bi-frontally during encoding, could modulate declarative memory performance, measured immediately after encoding, and after a night's sleep. An associative word-pair learning test was used. During an evening encoding phase, participants received 1 mA 140 Hz tACS or sham stimulation over both DLPFCs for 10 min while being presented twice with a list of word-pairs. Cued recall performance was investigated 10 min after training and the morning following the training session. Forgetting from evening to morning was observed in the sham condition, but not in the 140 Hz stimulation condition. 140 Hz tACS during encoding may have an effect on the consolidation of declarative material.
Estimating the Prevalence of Schizophrenia Among New Zealand Māori: A Capture–Recapture Approach

Objective: The aim of the present study was to estimate the 12 month prevalence of schizophrenia in the Māori population of New Zealand. Method: Mental health data from two national sources were obtained for the period 2000–2003. A simple count of unique individuals with schizophrenia was used to estimate contact prevalence and a four-list capture–recapture procedure to estimate population prevalence. Results: Contact prevalence was significantly lower than the estimated population prevalence for both groups. The estimated 12 month prevalence of schizophrenia for Māori (0.97%) was significantly higher than for non-Māori (0.32%), even after adjustment for age, case under-ascertainment, and socioeconomic deprivation. Conclusions: The prevalence of schizophrenia among Māori appears to be elevated, although limitations in diagnostic reliability and recording of ethnicity must be considered. This adds further evidence of worldwide variation in the prevalence of schizophrenia. Capture–recapture provides a reliable cost-effective alternative to epidemiological surveys for estimating the prevalence of low-prevalence disorders such as schizophrenia.
Evaluation of Cache Assisted Multithreaded Architecture

Solutions to the increasing memory latency problem fall into two categories. Latency avoidance uses caches to keep the most commonly accessed locations within immediate reach of the processor. A multilevel cache system can reduce the miss rate to 1% or less; even so, cache misses are expensive, producing processor idle times that can exceed 50% [15]. Latency tolerance tries to hide the latency by switching to another execution thread [4]. A relatively small number of threads is required to hide memory latency; however, the processor must maintain the state of each thread, thereby increasing its complexity.
Effect of Sodium Balance on Arterial Blood Pressure and Renal Responses to Prostaglandin A1 in Man

The effect of sodium balance on systemic arterial blood pressure and the renal response to intravenous infusion of prostaglandin A1 (PGA1) was studied in hypertensive subjects. PGA1 (0.4 μg/kg min−1) was infused for 1 hour in ten hypertensive subjects who were receiving a constant diet containing 40 mEq of sodium and 80 mEq of potassium. During PGA1 infusion a significant fall in both systolic and diastolic arterial blood pressure occurred. There was a significant rise in urine flow rate, renal plasma flow, and urine sodium excretion; plasma renin activity (PRA) rose slightly but not significantly. Eight of the ten subjects and one additional subject were then placed on furosemide (80 mg/day) for 1 week. In all subjects, a significant weight loss and a rise in midday PRA occurred with the administration of the diuretic. Systolic blood pressure fell, but diastolic pressure was unchanged. Following salt depletion with furosemide, PGA1 infusion studies were repeated. PGA1 then produced no significant change in systolic or diastolic blood pressure. Urine flow, renal plasma flow, and urine sodium excretion rose, but the degree of increase was markedly less than that observed prior to furosemide administration. In the salt-depleted subjects, a significant rise in PRA occurred during PGA1 infusion. The results indicate that volume depletion diminishes the systemic and renal hemodynamic response to infused PGA1 but enhances the PRA response. The increased PRA response during PGA1 infusion observed in saltdepleted subjects might in part account for the blunted hemodynamic changes. Alternatively, recent evidence indicates that the enhanced production of endogenous vasodilating prostaglandins which occurs in the salt-depleted state might account for the diminished hemodynamic responses to exogenous PGA1.
A rate-distortion theory for permutation spaces

We investigate the lossy compression of the permutation space by analyzing the trade-off between the size of a source code and the distortion with respect to either Kendall tau distance or ℓ1 distance of the inversion vectors. For both distortion measures, we characterize the rate-distortion functions and provide explicit code designs that achieve them. Finally, we provide bounds on the higher order terms in the codebook size when the distortion levels lead to degenerate code rates (0 or 1).