Miracle-dz/UniFAR-FTUs huggingface dataset:
Cognitive changes in asymptomatic drug-naïve human immunodeficiency virus type 1 clade C infection

Asymptomatic human immunodeficiency virus (HIV) infection is associated with impaired cognitive functioning in both clade B and C infections. The nature of cognitive change longitudinally has not been studied in asymptomatic clade C infection. The present study evaluated changes in neuropsychological functioning over a 21/2-year period in a cohort of HIV-1 clade C-infected asymptomatic individuals from South India. Participants with CD4 counts below 250 were started on highly active antiretroviral therapy (HAART) as per National AIDS Control Organisation (NACO) guidelines and hence excluded. The sample consisted of 68 patients (30 men and 38 women), with a mean age of 29.4 years (SD = 5.6 years) and a mean education of 10.0 years (SD =2.7 years). A comprehensive neuropsychological assessment with 12 tests yielding 21 variables was used to examine cognitive functioning at baseline and subsequently at 6-monthly intervals for five follow-ups. Shift in CD4 and viral load categories measured by the McNemar’s test indicated disease progression. Latent growth curve (LGC) modeling assessed the nature of change in cognition over the 21/2-year study period. Ten variables representing attention, executive functions, and long-term memory fit the LGC model. Excepting visual working memory, the slope was nonsignificant for nine variables, indicating absence of deterioration in cognition over a 21/2-year period. However, CD4 and viral load levels worsened, indicating disease progression. Asymptomatic individuals with HIV-1 clade C infection do not show any significant decline on individual neuropsychological functions over 21/2 years despite disease progression, as evidenced by immune suppression and viral loads.
Constrained discriminative PLDA training for speaker verification

Many studies have proven the effectiveness of discriminative training for speaker verification based on probabilistic linear discriminative analysis (PLDA) with i-vectors as features. Most of them directly optimize the log-likelihood ratio score function of the PLDA model instead of explicitly train the PLDA model. But this optimization process removes some of the constraints that normally are imposed on the PLDA log likelihood ratio score function. This may deteriorate the verification performance when the amount of training data is limited. In this paper, we first show two constraints which the score function should follow, and then we propose a new constrained discriminative training algorithm which keeps these constraints. Our experiments show that our method obtained significant improvements in the verification performance in the male trials of the telephone speaker verification tasks of NIST SRE08 and SRE10.
Carbon and nitrogen in forest floor and mineral soil under four forest species in the Mediterranean region

The organic and mineral horizons of soils are of great importance in C and N storage in forest areas. However, knowledge of the effects of forest species on the stocks of these elements is still scarce, especially in Portugal. In order to contribute to this knowledge, a study was carried out in forest stands of Pinus pinaster Aiton (PP), Pinus nigra Arnold (PN), Pseudotsuga menziesii (PM) and Castanea sativa Miller (CS), installed in the 1950s in northern Portugal. Sampling areas with similar topography, lithology and climate were selected, in order to better identify hypothesized differences in C and N storage due to forest species effect. In each stand, 15 sites were selected randomly and the forest floor (organic layers) was collected in a 0.49 m2 area. The layers H, L and F of the forest floor were identified and, for L and F, their components were separated in leaves, pine cones/chestnut husks and branches. At the same sites, soil samples were also collected at 0-10 and 10-20 cm depth. At these depths, undisturbed samples were also collected for bulk density determination. The concentrations of C and N were determined in forest floor and mineral components of the soil, and converted in mass per unit area. The quantity of C storage per unit area followed the sequence PN > PM > CS > PP, while for N the sequence was CS > PM > PN > PP, OM and PP keeping the same relative position in the sequence in both C and N concentrations. The PM and CS species store similar amounts of C and N, and about 90% of these elements is found in the upper 20 cm of the mineral soil. In PN and PP species, the contribution of forest floor to the storage of these elements is more expressive than in the other species, but lower than 30% in all cases.
Immortalized human corneal epithelial cells for ocular toxicity and inflammation studies.

PURPOSE To develop a metabolically competent, human immortalized corneal epithelial cell line for use in toxicity and inflammation studies. METHODS Primary corneal epithelial cells (P-CEPI) were immortalized by a recombinant simian virus (SV)40 T antigen retroviral vector defective for viral replication. The cells were grown in serum-free medium with the addition of bovine pituitary extract, cloned at passage 15 and one of the best-growing clones, CEPI-17-CL4, was extensively characterized for differentiation and metabolic characteristics of the human corneal epithelium. Methods used were immunostaining, reverse transcription-polymerase chain reaction (RT-PCR), northern blot analysis, and enzyme assays. RESULTS The CEPI-17-CL4 cells showed a typical cobblestone morphology, grew to more than 200 passages and expressed the SV40 T antigen in the nucleus of every cell. Immunofluorescence staining for CEPI-17-CL4 cells was strongly positive for keratins (K)8, K18, and K19 and vimentin; weakly positive for K3, K13, and K17; and negative for K4, K7, and K14. Expression of cytokines (interleukin [IL]-1alpha, IL-1beta, IL-6, IL-8, tumor necrosis factor-alpha, and IL-ra), growth factors (transforming growth factor [TGF]-alpha, epidermal growth factors [EGF], EGF receptor [EGFR], TGF-beta1, TGF-beta2, and platelet-derived growth factor-beta) and cytochrome P450 enzymes (1A1, 2C, 2E1, and 3A5) was similar in CEPI-17-CL4 cells and human corneal epithelial samples obtained in biopsy. The CEPI-17-CL4 cells were metabolically competent for enzymes glutathione S-transferase, quinone reductase, aflatoxin aldehyde reductase, glutathione peroxidase, glutathione reductase, superoxide dismutase, and catalase. CONCLUSIONS The CEPI-17-CL4 cells are truly immortal and express an extensive array of cytokines, growth factors, and metabolic enzymes that resemble the original tissue. These characteristics, which remain stable up to high passage, will allow reproducible, mechanistic studies on toxicity, inflammation, and wound healing.
Forward-Backward Activation Algorithm for Hierarchical Hidden Markov Models

Hierarchical Hidden Markov Models (HHMMs) are sophisticated stochastic models that enable us to capture a hierarchical context characterization of sequence data. However, existing HHMM parameter estimation methods require large computations of time complexity O(TN2D) at least for model inference, where D is the depth of the hierarchy, N is the number of states in each level, and T is the sequence length. In this paper, we propose a new inference method of HHMMs for which the time complexity is O(TND+1). A key idea of our algorithm is application of the forward-backward algorithm to state activation probabilities. The notion of a state activation, which offers a simple formalization of the hierarchical transition behavior of HHMMs, enables us to conduct model inference efficiently. We present some experiments to demonstrate that our proposed method works more efficiently to estimate HHMM parameters than do some existing methods such as the flattening method and Gibbs sampling method.
Estimate faction of photosynthetically active radiation with three-band vegetation indices based on HJ-CDD satellite in wheat

The fraction of absorbed photosynthetically active radiation (FPAR) is a key biophysical variable that can be used to derive agronomic information for crop condition monitoring and yield prediction. Vegetation indices have been proved to be a useful method for FPAR estimation. However, most vegetation indices have their own limitations and can decrease the sensitivity to FPAR. The object of this study is that three new vegetation indices, a characteristic of three-band vegetation indices with green band, were tested to estimate green part of FPAR (FPARgreen) and aim at improving the accuracy of FPAR estimation. These vegetation indices are Revised NDVI (RevNDVI), Added green band NDVI (AgbNDVI) and Mean and standard deviation-band vegetation index (MSVI). The top-of canopy (TOC) reflectance and FPAR were simulated by the PROSAIL radiative transfer model. The relationships between these vegetation indices and FPAR were performed and then the results were compared with the vegetation indices of NDVI, Green NDVI and WDRVI. A global sensitivity analysis (GSA) approach, the Extended Fourier Amplitude Sensitivity Test (EFAST) method, was used to determine the key impact factor of each vegetation index based on simulated crop canopy reflectance (PROSAIL). Validation study was also conducted using the ground measurements in wheat. The results show that the three new vegetation indices had significant sensitive to FPAR with high correlation coefficients. Both AgbNDVI and RevNDVI are more sensitivity to green part of plants and leaf chlorophyll content, and the AgbNDVI was better than RevNDVI. The result indicated that it will have a benefit for increasing accuracy of FPARgreen retrieving by AgbNDVI or RevNDVI.
When would this bug get reported?

Not all bugs in software would be experienced and reported by end users right away: Some bugs manifest themselves quickly and may be reported by users a few days after they get into the code base; others manifest many months or even years later, and may only be experienced and reported by a small number of users. We refer to the period of time between the time when a bug is introduced into code and the time when it is reported by a user as bug reporting latency. Knowledge of bug reporting latencies has an implication on prioritization of bug fixing activities-bugs with low reporting latencies may be fixed earlier than those with high latencies to shift debugging resources towards bugs highly concerning users. To investigate bug reporting latencies, we analyze bugs from three Java software systems: AspectJ, Rhino, and Lucene. We extract bug reporting data from their version control repositories and bug tracking systems, identify bug locations based on bug fixes, and back-trace bug introducing time based on change histories of the buggy code. Also, we remove non-essential changes, and most importantly, recover root causes of bugs from their treatments/fixes. We then calculate the bug reporting latencies, and find that bugs have diverse reporting latencies. Based on the calculated reporting latencies and features we extract from bugs, we build classification models that can predict whether a bug would be reported early (within 30 days) or later, which may be helpful for prioritizing bug fixing activities. Our evaluation on the three software systems shows that our bug reporting latency prediction models could achieve an AUC (Area Under the Receiving Operating Characteristics Curve) of 70.869%.
Attention versus Intention in the Primate Premotor Cortex

One challenging issue in cognitive neuroscience has been to dissociate a variety of mental processes from one another in order to elucidate brain functions. Attention, in particular, has been a recurrent issue because of its strong links with perceptual, cognitive, and motor performances. This paper reviews data from neurophysiological experiments designed to dissociate neuronal activity related to visuo-spatial attention from preparatory activity in the monkey brain. Cell activity was recorded from the dorsal premotor area (PMd) and compared to the dorsolateral prefrontal cortex (DLPf), from which it receives inputs. PMd has been implicated in the planing and execution of voluntary movements (PMd), and the majority of its cells are active during tasks with instructed delay time. However, the activity of many PMd cells is not specifically correlated with movement preparation, as is observed when the animal is attending to a visual stimulus, although the proportion of attention-related cells is much lower than in the DLPf. The distribution of attention-related and intention-related neurons within PMd tends to vary along the rostrocaudal axis, with the former more frequent rostrally (PMdr) and the latter more predominant caudally (PMdc). In a functional magnetic resonance imaging (fMRI) study in humans, we compared the premotor activation in two tasks: a spatial attention/memory task and a motor preparation task. The results suggest a rostrocaudal specialization within PMd of the human brain, with attention-related activation rostrally and medially and intention-related activation caudally. These studies indicate strong similarities in the functional organization of dorsal premotor cortex of human and monkey.
Clinical Evaluation of Macrolide-Resistant Mycoplasma pneumoniae

ABSTRACT Macrolide-resistant Mycoplasma pneumoniae (MR M. pneumoniae) has been isolated from clinical specimens in Japan since 2000. A comparative study was carried out to determine whether or not macrolides are effective in treating patients infected with MR M. pneumoniae. The clinical courses of 11 patients with MR M. pneumoniae infection (MR patients) treated with macrolides were compared with those of 26 patients with macrolide-susceptible M. pneumoniae infection (MS patients). The total febrile days and the number of febrile days during macrolide administration were longer in the MR patients than in the MS patients (median of 8 days versus median of 5 days [P = 0.019] and 3 days versus 1 day [P = 0.002], respectively). In addition, the MR patients were more likely than the MS patients to have had a change of the initially prescribed macrolide to another antimicrobial agent (63.6% versus 3.8%; odds ratio, 43.8; P < 0.001), which might reflect the pediatrician's judgment that the initially prescribed macrolide was not sufficiently effective in these patients. Despite the fact that the febrile period was prolonged in MR patients given macrolides, the fever resolved even when the initial prescription was not changed. These results show that macrolides are certainly less effective in MR patients.
design and optimization of automotive cardan shafts for industrial applications with enhanced performance and durability

A crucial part of a locomotive is the cardan shaft. A rear-wheel-drive vehicle's differential gear receives power from the engine through a spinning shaft known as a cardan shaft. The cardan shaft must turn at ever-changing angles between the gearbox and axle in order to function. High vibrations are experienced on it as a result of the constant rotation. This issue causes shafts to flex or distort. In this study, a cardan shaft's design and development are carried out. Although it is extensively beneficial in the locomotive industry, vibration is a significant issue with cardan shafts. Creo parametric software was used for developing the design, while Ansys was used to analyze it. Using Ansys software's modal analysis, verify the natural frequency. It is then contrasted with the different shaft cut-out geometries.
The role of gonadal hormones in neuromuscular synapse elimination in rats. I. Androgen delays the loss of multiple innervation in the levator ani muscle

The normal period of synapse elimination in the androgen-sensitive levator ani (LA) muscle occurs between 2 and 4 weeks after birth, well after the period of synapse elimination for most other rat muscles. To evaluate whether gonadal androgen might be involved in the delayed development of single innervation in the LA, we compared the time course of synapse elimination in LA muscles that lacked endogenous gonadal androgen or were exposed to exogenous androgen. Tetranitroblue tetrazolium was used to stain neuromuscular connections. Our results suggest that both endogenous and exogenous androgen delay the normal process of synapse elimination. Removing endogenous androgen resulted in lower levels of multiple innervation in the LA, suggesting that androgen may normally influence synapse elimination. Moreover, androgen treatment prevented much of the normal loss of multiple innervation in the LA. Androgen treatment during the normal period of synapse elimination also increased the diameter of LA muscle fibers, enhanced the development of preterminal branching, and increased the number of junctional sites on some LA fibers. Because androgen did not appear to induce the formation of new synapses through sprouting, we conclude that androgen maintained multiple innervation in the LA by preventing the normal ontogenetic process of synapse elimination.
Lack of Lipotoxicity Effect on β-Cell Dysfunction in Ketosis-Prone Type 2 Diabetes

OBJECTIVE Over half of newly diagnosed obese African Americans with diabetic ketoacidosis (DKA) discontinue insulin therapy and go through a period of near-normoglycemia remission. This subtype of diabetes is known as ketosis-prone type 2 diabetes (KPDM). RESEARCH DESIGN AND METHODS To investigate the role of lipotoxicity on β-cell function, eight obese African Americans with KPDM, eight obese subjects with type 2 diabetes with severe hyperglycemia without ketosis (ketosis-resistant type 2 diabetes), and nine nondiabetic obese control subjects underwent intravenous infusion of 20% intralipid at 40 ml/h for 48 h. β-Cell function was assessed by changes in insulin and C-peptide concentration during infusions and by changes in acute insulin response to arginine stimulation (AIRarg) before and after lipid infusion. RESULTS The mean time to discontinue insulin therapy was 11.0 ± 8.0 weeks in KPDM and 9.6 ± 2.2 weeks in ketosis-resistant type 2 diabetes (P = NS). At remission, KPDM and ketosis-resistant type 2 diabetes had similar glucose (94 ± 14 vs. 109 ± 20 mg/dl), A1C (5.7 ± 0.4 vs. 6.3 ± 1.1%), and baseline AIRarg response (34.8 ± 30 vs. 64 ± 69 μU/ml). P = NS despite a fourfold increase in free fatty acid (FFA) levels (0.4 ± 0.3 to 1.8 ± 1.1 mmol/l, P < 0.01) during the 48-h intralipid infusion; the response to AIRarg stimulation, as well as changes in insulin and C-peptide levels, were similar among obese patients with KPDM, patients with ketosis-resistant type 2 diabetes, and nondiabetic control subjects. CONCLUSIONS Near-normoglycemia remission in obese African American patients with KPDM and ketosis-resistant type 2 diabetes is associated with a remarkable recovery in basal and stimulated insulin secretion. A high FFA level by intralipid infusion for 48 h was not associated with β-cell decompensation (lipotoxicity) in KPDM patients.
Expression and antigenicity of virus‐like particles of norovirus and their application for detection of noroviruses in stool samples

Human noroviruses (NoVs), members of the genus Norovirus in the family Caliciviridae, are the leading agents of nonbacterial acute gastroenteritis worldwide. Human NoVs are currently divided into at least two genogroups, genogroup I (GI) and genogroup II (GII), each of which contains at least 14 and 17 genotypes. To explore the genetic and antigenic relationship among NoVs, we expressed the capsid protein of four genetically distinct NoVs, the GI/3 Kashiwa645 virus, the GII/3 Sanbu809 virus, the GII/5 Ichikawa754 virus, and the GII/7 Osaka10‐25 virus in baculovirus expression system. An antigen enzyme‐linked immunosorbent assay (ELISA) with hyperimmune serum against the four recombinant capsid proteins and characterized previously three capsid proteins derived from GI/1, GI/4, and GII/12 was developed to detect the NoVs antigen in stools. The antigen ELISA was highly specific to the homotypic strains, allowing assignment of a strain to a Norovirus genetic cluster within a genogroup. J. Med. Virol. 76:129–136, 2005. © 2005 Wiley‐Liss, Inc.
Diagnostic Assessment of Bone Marrow Aspiration Smears, Touch Imprints and Trephine Biopsy in Haematological Disorders

Diagnostic Assessment of bone marrow aspirate particle smears, imprints and biopsy sections was done on 40 haematological disorders. Core needle biopsy of the bone marrow is a safe and useful procedure. It is a valuable diagnostic aid for measurement of marrow cellularity and fibrosis.Bilateral trephine biopsy was conducted wherever necessary.Bone marrow aspiration was the most effective method for studying morphological details and was able to diagnose most of the cases except the 2 cases of myelofibrosis which yielded dry tap for which trephine biopsy was diagnostic.Trephine biopsy was also found to be superior for staging of lymphomas and to study the ALIP in MDS.Touch imprints were useful for studying cell morphology, where aspiration yielded dry tap.All the three procedures of bone marrow aspiration, trephine biopsy and touch imprints were found to be complementary to each other and superiority of one method over the other depended on the specific disease process.
When paxos meets erasure code: reduce network and storage cost in state machine replication

Paxos-based state machine replication is a key technique to build highly reliable and available distributed services, such as lock servers, databases and other data storage systems. Paxos can tolerate any minority number of node crashes in an asynchronous network environment. Traditionally, Paxos is used to perform a full copy replication across all participants. However, full copy is expensive both in term of network and storage cost, especially in wide area with commodity hard drives. In this paper, we discussed the non-triviality and feasibility of combining erasure code into Paxos protocol, and presented an improved protocol named RS-Paxos (Reed Solomon Paxos). To the best of our knowledge, we are the first to propose such a combination. Compared to Paxos, RS-Paxos requires a limitation on the number of possible failures. If the number of tolerated failures decreases by 1, RS-Paxos can save over 50% of network transmission and disk I/O. To demonstrate the benefits of our protocol, we designed and built a key-value store based on RS-Paxos, and evaluated it on EC2 with various settings. Experiment results show that RS-Paxos achieves at most 2.5x improvement on write throughput and as much as 30% reduction on latency, in common configurations.