Miracle-dz/UniFAR-FTUs huggingface dataset:
Therapeutic vaccines against HIV infection

Resistance to medication, adverse effects in the medium-to-long-term and cost all place important limitations on lifelong adherence to combined antiretroviral therapy (cART). In this context, new therapeutic alternatives to cART for life in HIV-infected patients merit investigation. Some data suggest that strong T cell-mediated immunity to HIV can indeed limit virus replication and protect against CD4 depletion and disease progression. The combination of cART with immune therapy to restore and/or boost immune-specific responses to HIV has been proposed, the ultimate aim being to achieve a functional cure. In this scenario, new, induced, HIV-specific immune responses would be able to control viral replication to undetectable levels, mimicking the situation of the minority of patients who control viral replication without treatment and do not progress to AIDS. Classical approaches such as whole inactivated virus or recombinant protein initially proved useful as therapeutic vaccines. Overall, however, the ability of these early vaccines to increase HIV-specific responses was very limited and study results were discouraging, as no consistent immunogenicity was demonstrated and there was no clear impact on viral load. Recent years have seen the development of new approaches based on more innovative vectors such as DNA, recombinant virus or dendritic cells. Most clinical trials of these new vectors have demonstrated their ability to induce HIV-specific immune responses, although they show very limited efficacy in terms of controlling viral replication. However, some preliminary results suggest that dendritic cell-based vaccines are the most promising candidates. To improve the effectiveness of these vaccines, a better understanding of the mechanisms of protection, virological control and immune deterioration is required; without this knowledge, an efficacious therapeutic vaccine will remain elusive.
The monoclonal antibody MAC387 detects an epitope on the calcium‐binding protein MRP14

The present study was initiated to identify the antigen recognized by the monoclonal antibody (MAb) MAC387 which is widely used for phenotypical characterization of myelomonocytic cells in situ. MAC387 has been described to show a similar reaction pattern as antisera to a complex formed by the calcium‐binding proteins MRP8 and MRP14. However, the exact nature of the molecule recognized by MAC387 has been controversial. Using Western blot analysis, MAC387 was found to detect a single protein band of 14 kDa in lysates of human monocytes and granulocytes. Transfection of embryonic lung fibroblasts L132 with either MRP8 or MRP14 cDNA revealed that MAC387 reacts with MRP14 but not MRP8. This finding was confirmed by dot blot analysis of recombinant MRP8 and MRP14. Our data thus provide unequivocal evidence that MAC387 is a monoclonal antibody directed against the calcium‐binding protein MRP14. J. Leukoc. Biol. 55: 259–261; 1994.
Multiaxial Fatigue Damage Models

Two multiaxial damage parameters are proposed in this paper. The proposed fatigue damage parameters do not include any weight constants, which can be used under either multiaxial proportional loading or non-proportional loading. On the basis of the research on the critical plane approach for the tension-torsion thin tubular multiaxial fatigue specimens, two multiaxial fatigue damage models are proposed by combining the maximum shear strain and the normal strain excursion between adjacent turning points of the maximum shear strain on the critical plane. The proposed multiaxial fatigue damage models are used to predict the fatigue lives of the tension-torsion thin tube, and the results show that a good agreement is demonstrated with experimental data.
The Effects of Operational Conditions on the Respiration Rate of Tubificidae

Tubificidae is often used in the wastewater treatment systems to minimize the sludge production because it can be fed on the activated sludge. The process conditions have effect on the growth, reproduction, and sludge reduction efficiency of Tubificidae. The effects of the water quality, density of worms, pH, temperature and dissolved oxygen (DO) concentration on the respiration rate of Tubificidae were investigated to determine the optimal conditions for the growth and metabolism of the worms and reveal the mechanisms involving the efficient sludge reduction in terms of these conditions. It was observed that the respiration rate was highest in the water discharged from an ecosystem that included symbiotic Tubificidae and microbes and was lowest in distilled water. Considering density of the worms, the highest rate was 81.72±5.12 mg O2/g(dry weight)·h·L with 0.25 g (wet weight) of worms in 1 L test flask. The maximum Tubificidae respiration rate was observed at a pH of 8.0±0.05, a rate that was more than twice as high as those observed at other pH values. The respiration rate increased in the temperature range of ∼8°C–22°C, whereas the rate declined in the temperature range of ∼22°C–30°C. The respiration rate of Tubificidae was very high for DO range of ∼3.5–4.5 mg/L, and the rates were relatively low for out of this DO range. The results of this study revealed the process conditions which influenced the growth, and reproduction of Tubificidae and sludge reduction at a microscopic level, which could be a theoretical basis for the cultivation and application of Tubificidae in wastewater treatment plants.
Hippocampal/amygdala volumes in geriatric depression

Background. The hippocampus, amygdala and related functional circuits have been implicated in the regulation of emotional expression and memory processes, which are affected in major depression. Several recent investigations have reported abnormalities in these structures in adult and elderly depressives. Methods. Elderly DSM-III-R unipolar depressives (N=40) and normal controls (N=46) participated in a magnetic resonance imaging study (1.0T). Brain images were obtained in the coronal plane. Using established anatomical guidelines for structure delineation, volumetric measurements of left and right hippocampus and anterior hippocampus/amygdala complex were completed under blinded conditions using a semi-automated computer mensuration system, with patients and controls in random order. Results. Medial temporal volumes did not significantly distinguish either elderly depressed and age-similar normal control subjects, or late onset and early onset depressed patients (ANCOVA). Major overlap of measured volumes existed between patient and control groups. In depressives, hippocampal volumes significantly correlated with age, and cognitive and depression ratings, but not with number of prior depressive episodes or age-at-onset of first depression. Conclusions. Hippocampal volumes do not discriminate a typical clinical population of elderly depressed patients from age-similar normal control subjects. If hippocampal dysfunction contributes to a diagnosis of syndromal depression in the elderly, such dysfunction does not appear to be regularly reflected in structural abnormalities captured by volumetric measurement as conducted. On the other hand, relationships between hippocampal volumes and clinical phenomena in depressives, but not controls, suggest potentially meaningful interactions between hippocampal structure and the expression of major depression in the elderly.
Evaluation of durability tests for permeable friction course mixtures

Durability of porous or permeable friction courses (PFC) is an important aspect to address when designing this type of hot mix asphalt. At present, several agencies perform the mix design of PFC primarily by determining volumetric mixture properties. This approach ensures adequate mixture functionality, but it does not guarantee mixture durability. This paper evaluates the Cantabro loss test, the Hamburg Wheel-Tracking test (HWTT) and the Overlay test (OT) to determine the one most appropriate for mix design and laboratory performance evaluations. The Cantabro loss test, performed in both dry and wet conditions, is recommended for PFC mix design to corroborate the suitability of the optimum asphalt content defined based on volumetric determinations. The HWTT and the OT are not recommended, since the variability of the test results indicated that these tests may not be suitable for PFC mixtures.
Current concepts in the pathogenesis of alcoholic liver injury

Alcoholic liver disease (ALD) develops as a consequence of priming and sensitizing mecha nisms rendered by cross‐interactions of primary mech anistic factors and secondary risk factors. This concept, albeit not novel, is becoming widely accepted by the field, and more research is directed toward identifying and characterizing the interfaces of the cross‐interactions to help understand individual predisposition to the disease. Another pivotal development is the begin ning of cell type‐specific research to elucidate specific contributions not only of hepatocytes, but also of hepatic macrophages, liver‐associated lymphocytes, si nusoidal endothelial cells, and hepatic stellate cells to sensitizing and priming mechanisms. In particular, the critical role of hepatic macrophages has been high lighted and the priming mechanisms concerning this paracrine effect have been proposed. Glutathione de pletion in hepatocyte mitochondria is considered the most important sensitizing mechanism. One of the contributing factors is decreased methionine metabo lism. Remaining key questions include how altered methionine metabolism contribute to the pathogenesis of ALD; how cross‐talk among nonparenchymal liver cells or between nonparenchymal cells and hepatocytes leads to ALD; how dysfunctional mitochondria deter mine the type of cell death in ALD; and what secondary factors are critical for the development of advanced ALD such as alcoholic hepatitis and cirrhosis. —Tsukamoto, H. , Lu, S. C. Current concepts in the pathogenesis of alcoholic liver injury. The FASEB J. 15, 1335–1349 (2001)
Integrated OR/CP optimization for Discrete Event Systems with nonlinear cost

Optimization of a discrete event systems including (non)linear cost in local states is mainly solved either by heuristic search methods or mathematical programming. In this paper the second approach is further elaborated, including guarantees on both optimal performance and logical correctness. An integrated algorithm is developed utilizing both Operations Research (OR) and Constraint Programming (CP). The majority of integrated approaches have up till now focused on solving linear problems. In this paper we use our integrated algorithm to optimize discrete event systems with nonlinear cost and logical constraints. We present a straightforward method to incorporate OR functionality into an existing CP algorithm such that it can process nonlinear expressions, otherwise too complex for the CP algorithm to handle. Evaluation of the algorithm's performance is done by comparison to that of state of the art Mixed Integer Nonlinear Programming (MINLP) methods. The benchmark shows that our integrated approach finds the optimal solution in roughly the same time as existing MINLP methods. However, when also proof of optimality is required, the integrated algorithm outperforms the best MINLP algorithm by roughly a factor of ten.
miR-29b attenuates tumorigenicity and stemness maintenance in human glioblastoma multiforme by directly targeting BCL2L2

Glioblastoma multiforme (GBM) is the most common malignant brain tumor and exhibits aggressive and invasive behavior. We previously identified four miRNAs—miR-29b, 494, 193a-3p, and 30e—with enhanced expression in GBM following treatment of ionizing radiation by miRNA microarray analysis. In this study, we found that only miR-29b inhibited tumor cell migration and invasion by reducing MMP-2 activity via phospho-AKT/β-catenin signaling, and stimulated a more epithelial-like morphology. Moreover, miR-29b inhibits angiogenesis by attenuating tube formation and the expression of VEGF and Ang-2, and stemness maintenance in GBM cells, as demonstrated by decreasing neurosphere formation and cancer stem cell marker protein expression. These findings support the anti-tumor properties of miR-29b in human GBM cells. Furthermore, miR-29b expression was inversely proportional to that of BCL2L2 mRNA or protein in various cancer cell types. Interestingly, BCL2L2 mRNA is highly expressed in the mesenchymal type of GBM. To further elucidate the relationship between miR-29b and BCL2L2 in GBM, we performed co-transfection reporter assays and determined that miR-29b downregulates BCL2L2 expression by directly binding its 3′UTR. Finally, we confirmed that BCL2L2 repression is of central importance to miR-29b anti-tumor activity using functional assays to examine cell migration, invasion, angiogenesis, and stemness. From these data, we propose that miR-29b may be a useful therapeutic agent in GBM.
Sirtuin‐independent effects of nicotinamide on lifespan extension from calorie restriction in yeast

Two models have been proposed for how calorie restriction (CR) enhances replicative longevity in yeast: (i) suppression of rDNA recombination through activation of the sirtuin protein deacetylase Sir2 or (ii) decreased activity of the nutrient‐responsive kinases Sch9 and TOR. We report here that CR increases lifespan independently of all Sir2‐family proteins in yeast. Furthermore, we demonstrate that nicotinamide, an inhibitor of Sir2‐mediated deacetylation, interferes with lifespan extension from CR, but does so independent of Sir2, Hst1, Hst2, and Hst4. We also find that 5 mm nicotinamide, a concentration sufficient to inhibit other sirtuins, does not phenocopy deletion of HST3. Thus, we propose that lifespan extension by CR is independent of sirtuins and that nicotinamide has sirtuin‐independent effects on lifespan extension by CR.
Parenting Services May Be an Opportunity for Improving Bedtime Routines Among At-Risk Preschoolers

Several interventions aimed at improving children's sleep behaviors have been successful. However, a less expensive alternative with broader coverage might be for existing parenting programs to incorporate sleep promotion into their curricula. This study examines approximately 1,800 low-income children according to whether their mothers received 5 types of parenting services in the child's first 3 years of life: case management, home visiting, parent–child groups, parenting classes, and parenting support groups. Children whose mothers participated in a parent–child group or parenting class by the child's 10th month of life, or in case management between the child's 11th and 19th months of life, were more likely to have a regular bedtime at age 3. Children whose mother participated in a parent–child group between the child's 11th and 19th months of life were more likely to have a regular bedtime routine (i.e., bathing or reading a story) at age 3. Home visiting and parent support groups were not associated with children's sleep-related behaviors. Further research should explore the potential for integrating sleep-related behaviors into the curriculum for case management, parent–child groups, and parenting classes in children's first 3 years of life.
CRYPTIC FEMALE PREFERENCE FOR COLORFUL MALES IN GUPPIES

Abstract Cryptic female choice (CFC) refers to female-mediated processes occurring during or after copulation that result in biased sperm use in favor of preferred or compatible males. Despite recent empirical support for this hypothesis, evidence that CFC contributes towards the evolution of male body ornaments, in the same way that precopulatory female choice does, is currently lacking. Here, we tested the possibility that CFC selects for increased male attractiveness in the guppy Poecilia reticulata, a freshwater fish exhibiting internal fertilization. Specifically, we examined whether females are able to manipulate the number of sperm transferred or retained at copulation in favor of relatively attractive males. In support of this prediction, we found that following solicited copulations the number of sperm inseminated is influenced exclusively by the female's perception of relative male coloration, independent of any direct manipulation of males themselves. Because females prefer brightly colored males during precopulatory mate choice, our finding that colorful males are also favored as a consequence of enhanced insemination success indicates that cryptic female choice can reinforce precopulatory preferences for extravagant male ornaments.
The lipid-transfer protein Nir2 enhances epithelial-mesenchymal transition and facilitates breast cancer metastasis

ABSTRACT The involvement of epithelial-mesenchymal transition (EMT) in breast cancer metastasis has been demonstrated in many studies. However, the intracellular proteins and signaling pathways that regulate EMT have not been fully identified. Here, we show that the lipid-transfer protein Nir2 (also known as PITPNM1) enhances EMT in mammary epithelial and breast cancer cells. Nir2 overexpression decreases the expression of epithelial markers and concomitantly increases the expression of mesenchymal markers, whereas silencing of Nir2 expression by small hairpin RNA (shRNA) has opposite effects. Additionally, Nir2 expression is increased during EMT and affects cell morphology, whereas Nir2 depletion attenuates growth factor-induced cell migration. These effects of Nir2 on EMT-associated processes are mainly mediated through the PI3K/AKT and the ERK1/2 pathways. Nir2 depletion also inhibits cell invasion in vitro and lung metastasis in animal models. Immunohistochemical analysis of breast cancer tissue samples reveals a correlation between high Nir2 expression and tumor grade, and Kaplan–Meier survival curves correlate Nir2 expression with poor disease outcome. These results suggest that Nir2 not only enhances EMT in vitro and breast cancer metastasis in animal models, but also contributes to breast cancer progression in human patients.
Predictor virtualization

Many hardware optimizations rely on collecting information about program behavior at runtime. This information is stored in lookup tables. To be accurate and effective, these optimizations usually require large dedicated on-chip tables. Although technology advances offer an increased amount of on-chip resources, these resources are allocated to increase the size of on-chip conventional cache hierarchies. This work proposes Predictor Virtualization, a technique that uses the existing memory hierarchy to emulate large predictor tables. We demonstrate the benefits of this technique by virtualizing a state-of-the-art data prefetcher. Full-system, cycle-accurate simulations demonstrate that the virtualized prefetcher preserves the performance benefits of the original design, while reducing the on-chip storage dedicated to the predictor table from 60KB down to less than one kilobyte.
High Performance Scientific Computing Using FPGAs with IEEE Floating Point and Logarithmic Arithmetic for Lattice QCD

The recent development of large FPGAs along with the availability of a variety of floating point cores have made it possible to implement high-performance matrix and vector kernel operations on FPGAs. In this paper we seek to evaluate the performance of FPGAs for real scientific computations by implementing Lattice QCD, one of the classic scientific computing problems. Lattice QCD is the focus of considerable research work worldwide, including two custom ASIC-based solutions. Our results give significant insights into the usefulness of FPGAs for scientific computing. We also seek to evaluate two different number systems available for running scientific computations on FPGAs. To do this we implement FPGA based lattice QCD processors using both double precision IEEE floating point and single precision equivalent Logarithmic Number System (LNS) cores and compare their performance with that of two lattice QCD targeted ASIC based solutions and with PC cluster based solutions.
Function of the Small Hydrophobic Protein of J Paramyxovirus

ABSTRACT At 18,954 nucleotides, the J paramyxovirus (JPV) genome is one of the largest in the family Paramyxoviridae, consisting of eight genes in the order 3′-N-P/V/C-M-F-SH-TM-G-L-5′. To study the function of novel paramyxovirus genes in JPV, a plasmid containing a full-length cDNA clone of the genome of JPV was constructed. In this study, the function of the small hydrophobic (SH) protein of JPV was examined by generating a recombinant JPV lacking the coding sequence of the SH protein (rJPVΔSH). rJPVΔSH was viable and had no growth defect in tissue culture cells. However, more tumor necrosis factor alpha (TNF-α) was produced during rJPVΔSH infection, suggesting that SH plays a role in inhibiting TNF-α production. rJPVΔSH induced more apoptosis in tissue culture cells than rJPV. Virus-induced apoptosis was inhibited by neutralizing antibody against TNF-α, suggesting that TNF-α contributes to JPV-induced apoptosis in vitro. The expression of JPV SH protein inhibited TNF-α-induced NF-κB activation in a reporter gene assay, suggesting that JPV SH protein can inhibit TNF-α signaling in vitro. Furthermore, infection of mice with rJPVΔSH induced more TNF-α expression, indicating that SH plays a role in blocking TNF-α expression in vivo.
A Model Approximation Scheme for Planning in Partially Observable Stochastic Domains

Partially observable Markov decision processes (POMDPs) are a natural model for planning problems where effects of actions are nondeterministic and the state of the world is not completely observable. It is difficult to solve POMDPs exactly. This paper proposes a new approximation scheme. The basic idea is to transform a POMDP into another one where additional information is provided by an oracle. The oracle informs the planning agent that the current state of the world is in a certain region. The transformed POMDP is consequently said to be region observable. It is easier to solve than the original POMDP. We propose to solve the transformed POMDP and use its optimal policy to construct an approximate policy for the original POMDP. By controlling the amount of additional information that the oracle provides, it is possible to find a proper tradeoff between computational time and approximation quality. In terms of algorithmic contributions, we study in details how to exploit region observability in solving the transformed POMDP. To facilitate the study, we also propose a new exact algorithm for general POMDPs. The algorithm is conceptually simple and yet is significantly more efficient than all previous exact algorithms.
Orthorexia Nervosa in Turkish Dietitians

The purpose of this study was to determine the prevalence of orthorexia nervosa in dietitians, as assessed by administering ORTO-15, Eating Attitudes Test-40 (EAT-40) and Maudsley Obsessive-Compulsive Inventory (MOCI). Our study included 117 dietitians (Ankara). Orto-15 test scores below 40 points was considered indicative of orthorexia, while higher scores indicated a normal eating behavior. It was found that participants with ORTO-15 scores less than 40 had higher scores for EAT-40 and MOCI (p < 0.05). The results showed a significant negative correlation between the ORTO-15 and EAT-40 scores and BMI values. In that respect, further investigation with dietitians into orthorexia nervosa is recommended.