Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutathione levels in human tumors

This review summarizes clinical studies in which glutathione was measured in tumor tissue from patients with brain, breast, gastrointestinal, gynecological, head and neck and lung cancer. Glutathione tends to be elevated in breast, ovarian, head and neck, and lung cancer and lower in brain and liver tumors compared to disease-free tissue. Cervical, colorectal, gastric, and esophageal cancers show both higher and lower levels of tumor glutathione. Some studies show an inverse relationship between patient survival and tumor glutathione. Based on this survey, we recommend approaches that may improve the clinical value of glutathione as a biomarker.
Online hot topic detection from web news archive in short terms

In the age of information explosion, vast amount of information is now available on the internet. Early warning of breaking events is becoming a popular subject to study. Timeliness is the one of the most important factors to be considered in this subject. However, traditional topic detection approaches are always not so effective for the detection of emerging topics which concentrate all the news stories in a short term that make up the breaking topics. Therefore, a specific approach that applies to topic detection in short terms is required for this subject. In this paper, we utilize a temporal distance factor to measure the similarity between news stories and topics and then propose a novel approach based on it that could perform better in short-term topic detection. In the meantime, the aging theory was adopted in our scheme to build the life cycle model of events, from which we can get access to the hotness ranking at any time and lay a foundation for the research on early warning of breaking topics in the future. The following experiments indicate that our approach is effective and the life cycle model of events can basically conform to the reality.
Regional MLEM reconstruction strategy for PET-based treatment verification in ion beam radiotherapy

In ion beam radiotherapy, PET-based treatment verification provides a consistency check of the delivered treatment with respect to a simulation based on the treatment planning. In this work the region-based MLEM reconstruction algorithm is proposed as a new evaluation strategy in PET-based treatment verification. The comparative evaluation is based on reconstructed PET images in selected regions, which are automatically identified on the expected PET images according to homogeneity in activity values. The strategy was tested on numerical and physical phantoms, simulating mismatches between the planned and measured β+ activity distributions. The region-based MLEM reconstruction was demonstrated to be robust against noise and the sensitivity of the strategy results were comparable to three voxel units, corresponding to 6 mm in numerical phantoms. The robustness of the region-based MLEM evaluation outperformed the voxel-based strategies. The potential of the proposed strategy was also retrospectively assessed on patient data and further clinical validation is envisioned.
Physical Training and Antiplatelet Treatment in Stage II Peripheral Arterial Occlusive Disease: Alone or Combined?

The efficacy of physical training alone or combined with antiplatelet thera py (dipyridamole and aspirin) was studied in 30 patients with stage II peripheral arterial occlusive disease (PAOD). Patients were randomly allocated to one of the following groups: Group A— dipyridamole 75 mg three times daily and aspirin 330 mg once daily: Group B— physical exercise; Group C—physical exercise and dipyridamole 75 mg three time daily and aspirin 330 mg once daily. After six months' treatment the pain-free walking time (PFWT) and the max imum walking time (MWT) improved significantly (p < 0.05) in all three groups. In group A the PFWT lengthened by 35% (from 101.00 ± 34.56 to 137.32 ± 40.50 s) and the MWT by 38% (from 150.34 ± 55.60 to 207.26 ± 60.67 s); in group B the PFWT lengthened by 90% (from 90.65 ± 40.54 to 171.45 ± 55.60 s) and the MWT by 86% (from 145.39 ± 60.50 to 270.63 ± 63.61 s). When physical exer cise was associated with drugs as in group C, the PFWT lengthened by 120% (from 89.51 ± 43.89 to 196.72 ±51.73 s) and the MWT by 105% (from 160.43 ± 59.84 to 329.05 ± 63.96 s). No significant variations were observed at any stage of the study in the ankle/arm pressure ratio at rest and after standard treadmill exercise, in the plethysmographic rest and peak flows, or in the trans cutaneous oxygen pressure in basal conditions and in its half recovery time after an induced ischemia. The results confirm the benefits of regular exercise in stage II PAOD pa tients but suggest they may be enhanced by antiplatelet therapy.
Immunomodulatory Effects of Everolimus in a Long Responsive Patient With Metastatic Renal Cell Carcinoma

Everolimus is an inhibitor of mammalian target of rapamycin, approved in patients with metastatic renal cell carcinoma. Besides, mammalian target of rapamycin inhibition has the ability to modulate T-lymphocyte homeostasis. Here, we report the case of a metastatic renal cell carcinoma patient treated with everolimus who presented unexpected prolonged tumor response. The monitoring of immune responses showed strong antitumor T-cell activation at the time of disease control, whereas a profound immunosuppression occurred when tumor progressed. Thus, a change of immune functions is associated with everolimus treatment. Our observation suggests that everolimus could shape immune responses, which in turn could contribute to its efficacy.
Glutamate decarboxylase-immunoreactive neurons are preserved in human epileptic hippocampus

The present study was designed to determine whether inhibitory neurons in human epileptic hippocampus are reduced in number, which could reduce inhibition on principal cells and thereby be a basis for seizure susceptibility. We studied the distribution of GABA neurons and puncta by using glutamate decarboxylase (GAD) immunocytochemistry (ICC) together with Nissl stains. Using quantitative comparisons of GAD- immunoreactive (GAD-IR) neurons and puncta in human epileptic hippocampus and in the normal monkey hippocampus, we found that GAD-IR neurons and puncta are relatively unaffected by the hippocampal sclerosis typical of hippocampal epilepsy where 50–90% of principal (non-GAD-IR) cells are lost. GAD-IR neurons and puncta were not significantly decreased compared with normal monkey. In 6 patients, prior in vivo electrophysiology demonstrated that the anterior hippocampus generated all seizures. The anterior and posterior hippocampus were processed simultaneously, and the counts of hippocampal GAD-IR neurons were numerically greater in anterior than in the posterior hippocampus, where no seizures were initiated. These results indicate that GABA neurons are intact in sclerotic and epileptogenic hippocampus. Computerized image analysis of puncta densities in fascia dentata, Ammon's horn, and subicular complex in epileptic hippocampi (n = 7) were not different from puncta densities in the same regions in normal monkey (n = 2). Hence, despite the significant loss of principal cells (50–90% loss) GABA terminals (GAD- IR puncta) were normal, which suggests GABA hyperinnervation of the remnant pyramidal cells and/or dendrites in human epileptic hippocampus. The apparent increase in puncta ranged from 2 (fascia dentata) to 3.3 (CA1) times normal puncta densities. These findings would suggest increased inhibition and less excitability; however, those regions were epileptogenic. We suggest that GABA terminal sprouting or hyperinnervation of the few remnant projection cells may serve to synchronize their membrane potentials so that subsequent excitatory inputs will trigger a larger population of neurons for seizure onset in the hippocampus and propagation out to undamaged regions of subiculum and neocortex.
JMC: Jitter-Based Mixed-Criticality Scheduling for Distributed Real-Time Systems

These days, the term of Internet of Things (IoT) becomes popular to interact and cooperate with individual smart objects, and one of the most critical challenges for IoT is to achieve efficient resource sharing as well as ensure safety-stringent timing constraints. To design such reliable real-time IoT, this paper focuses on the concept of mixed-criticality (MC) introduced to address the low processor utilization on traditional real-time systems. Although different worst-case execution time estimates depending on criticality are proven effective on processor scheduling, the MC concept is not yet mature on distributed systems (such as IoT), especially with end-to-end deadline guarantee. To the best of our knowledge, this paper presents the first attempt to apply the MC concept into interference (or jitter), which is a complicated source of pessimism when analyzing the schedulability of distributed systems. Our goal is to guarantee the end-to-end deadlines of high-criticality flows and minimize the deadline miss ratio of low-criticality flows in distributed systems. To achieve this goal, we introduce a jitter-based MC (JMC) scheduling framework, which supports node-level mode changes in distributed systems. We present an optimal feasibility condition (subject to given schedulability analysis) and two policies to determine jitter-threshold values to achieve the goal in different conditions. Via simulation results for randomly generated workloads, JMC outperforms an existing criticality-monotonic scheme in terms of achieving higher schedulability and fewer deadline misses.
Rhesus macaque antibody molecules: sequences and heterogeneity of alpha and gamma constant regions

Rhesus macaques (Macaca mulatta) are extensively used in vaccine development. Macaques infected with simian immunodeficiency viruses (SIV) or simian‐human immunodeficiency viruses (SHIV) are the best animal model currently available for acquired‐immune‐deficiency‐syndrome‐related studies. Recent results emphasize the importance of antibody responses in controlling HIV and SIV infection. Despite the increasing attention placed on humoral immunity in these models, very limited information is available on rhesus macaque antibody molecules. Therefore, we sequenced, cloned and characterized immunoglobulin gamma (IGHG) and alpha (IGHA) chain constant region genes from rhesus macaques of Indian and Chinese origin. Although it is currently thought that rhesus macaques express three IgG subclasses, we identified four IGHG genes, which were designated IGHG1, IGHG2, IGHG3 and IGHG4 on the basis of sequence similarities with the four human genes encoding the IgG1, IgG2, IgG3 and IgG4 subclasses. The four genes were expressed at least at the messenger RNA level, as demonstrated by real‐time reverse transcription polymerase chain reaction (RT‐PCR). The level of intraspecies heterogeneity was very high for IGHA genes, whereas IGHG genes were remarkably similar in all animals examined. However, single amino acid substitutions were present in IGHG2 and IGHG4 genes, indicating the presence of IgG polymorphism possibly resulting in the expression of different allotypes. Two IgA alleles were identified in several animals and RT‐PCR showed that both alleles may be expressed. Presence of immunoglobulin gene polymorphism appears to reflect the unusually high levels of intraspecies heterogeneity already demonstrated for major histocompatibility complex genes in this non‐human primate species.
Adenovirus infection among allogeneic stem cell transplant recipients

The human adenovirus (HAdV) infection can cause severe disease in immunocompromised patients, such as those undergoing allogeneic hematopoietic stem cell transplant (ASCT). The main objective of this study was to prospectively monitor ASCT recipients for HAdV occurrence in a reference center in Brazil, and also to correlate viral positivity, viral load, molecular variant, clinical symptoms, and patients’ prognosis. From October/2012 to October/2014, blood and feces of 21 ASCT recipients were screened for HAdV by Nested‐PCR. Viral loads were determined by real‐time PCR. In total, 57% of the patients had at least one positive sample (serum or feces) for HAdV. Patients presented significantly higher viral load in feces when compared to serum. Positive samples were characterized as HAdVs of species HAdV‐C, ‐D, and ‐F. The main clinical symptom presented by infected patients was diarrhea, and Graft‐versus‐host disease (GVHD) was the main intercurrence. An association was observed between HAdV‐positivity and diarrhea and also between HAdV‐positivity and GVHD. Results from this study may contribute to a better understanding of the HAdV infection pattern in patients submitted to ASCT. Data therein highlight the importance of including HAdV testing during all routine laboratory exams performed on ASCT patients. J. Med. Virol. 89:298–303, 2017. © 2016 Wiley Periodicals, Inc.
High-Level Aminoglycoside Resistance in the Beta-Hemolytic Group G Streptococcus Isolate BM2721

ABSTRACT The beta-hemolytic group G Streptococcus clinical isolate BM2721 was resistant to high levels of aminoglycosides by synthesis of AAC(6′)-APH(2"), APH(3′)-III, and ANT(6) modifying enzymes. The corresponding genes were found to be adjacent as the result of a recombination event between Tn4001 and Tn5405, two transposons originating in staphylococci.
Light-Regulated, Tissue-Specific, and Cell Differentiation-Specific Expression of the Arabidopsis Fe(III)-Chelate Reductase Gene AtFRO61

Iron is an essential element for almost all living organisms, actively involved in a variety of cellular activities. To acquire iron from soil, strategy I plants such as Arabidopsis (Arabidopsis thaliana) must first reduce ferric to ferrous iron by Fe(III)-chelate reductases (FROs). FRO genes display distinctive expression patterns in several plant species. However, regulation of FRO genes is not well understood. Here, we report a systematic characterization of the AtFRO6 expression during plant growth and development. AtFRO6, encoding a putative FRO, is specifically expressed in green-aerial tissues in a light-dependent manner. Analysis of mutant promoter-β-glucuronidase reporter genes in transgenic Arabidopsis plants revealed the presence of multiple light-responsive elements in the AtFRO6 promoter. These light-responsive elements may act synergistically to confer light responsiveness to the AtFRO6 promoter. Moreover, no AtFRO6 expression was detected in dedifferentiated green calli of the korrigan1-2 (kor1-2) mutant or undifferentiated calli derived from wild-type explants. Conversely, AtFRO6 is expressed in redifferentiated kor1-2 shoot-like structures and differentiating calli of wild-type explants. In addition, AtFRO7, but not AtFRO5 and AtFRO8, also shows a reduced expression level in kor1-2 green calli. These results suggest that whereas photosynthesis is necessary but not sufficient, both light and cell differentiation are necessary for AtFRO6 expression. We propose that AtFRO6 expression is light regulated in a tissue- or cell differentiation-specific manner to facilitate the acquisition of iron in response to distinctive developmental cues.
DPP4 gene variation affects GLP-1 secretion, insulin secretion, and glucose tolerance in humans with high body adiposity

Objective Dipeptidyl-peptidase 4 (DPP-4) cleaves and inactivates the insulinotropic hormones glucagon-like peptide 1 (GLP-1) and gastric inhibitory polypeptide, collectively termed incretins. DPP-4 inhibitors entered clinical practice as approved therapeutics for type-2 diabetes in 2006. However, inter-individual variance in the responsiveness to DPP-4 inhibitors was reported. Thus, we asked whether genetic variation in the DPP4 gene affects incretin levels, insulin secretion, and glucose tolerance in participants of the TÜbingen Family study for type-2 diabetes (TÜF). Research design and methods Fourteen common (minor allele frequencies ≥0.05) DPP4 tagging single nucleotide polymorphisms (SNPs) were genotyped in 1,976 non-diabetic TÜF participants characterized by oral glucose tolerance tests and bioimpedance measurements. In a subgroup of 168 subjects, plasma incretin levels were determined. Results We identified a variant, i.e., SNP rs6741949, in intron 2 of the DPP4 gene that, after correction for multiple comparisons and appropriate adjustment, revealed a significant genotype-body fat interaction effect on glucose-stimulated plasma GLP-1 levels (p = 0.0021). Notably, no genotype-BMI interaction effects were detected (p = 0.8). After stratification for body fat content, the SNP negatively affected glucose-stimulated GLP-1 levels (p = 0.0229), insulin secretion (p = 0.0061), and glucose tolerance (p = 0.0208) in subjects with high body fat content only. Conclusions A common variant, i.e., SNP rs6741949, in the DPP4 gene interacts with body adiposity and negatively affects glucose-stimulated GLP-1 levels, insulin secretion, and glucose tolerance. Whether this SNP underlies the reported inter-individual variance in responsiveness to DPP-4 inhibitors, at least in subjects with high body fat content, remains to be shown.
Exon sharing of a novel human zinc-finger gene, ZIM2, and paternally expressed gene 3 (PEG3).

We have identified a novel human gene, ZIM2 (zinc-finger gene 2 from imprinted domain), located 25 kb downstream of PEG3 (paternally expressed gene 3). ZIM2 produces two different-size transcripts, 2.5 and 9.0 kb in length, with highest levels of expression in adult testis and modest levels in fetal kidney and brain. The 2.5-kb transcript of ZIM2 consists of 11 exons and encodes a Kruppel-type (C2H2) zinc-finger protein with a conserved Kruppel-associated box (KRAB) domain. Rapid amplification of cDNA ends and cDNA sequencing studies showed that ZIM2 and PEG3 transcripts share identical 5'-ends, composed of 7 small exons. Alternative splicing events connect these 7 exons either with the remaining 2 exons of PEG3 or with the remaining 4 exons of ZIM2. Interestingly, the third among the 7 shared exons exhibits sequence similarity to leucine-rich domains that are found at the N-terminal region of a subset of KRAB-containing zinc-finger genes. Sequencing of the 5'-termini of both transcripts indicates that ZIM2 and PEG3 share identical transcription start sites and may also share upstream regulatory elements, although the two genes show distinct patterns of tissue-specific expression.
A New Member of the Sin3 Family of Corepressors Is Essential for Cell Viability and Required for Retroelement Propagation in Fission Yeast

ABSTRACT Tf1 is a long terminal repeat (LTR)-containing retrotransposon that propagates within the fission yeast Schizosaccharomyces pombe. LTR-retrotransposons possess significant similarity to retroviruses and therefore serve as retrovirus models. To determine what features of the host cell are important for the proliferation of this class of retroelements, we screened for mutations in host genes that reduced the transposition activity of Tf1. We report here the isolation and characterization of pst1+, a gene required for Tf1 transposition. The predicted amino acid sequence of Pst1p possessed high sequence homology with the Sin3 family of proteins, known for their interaction with histone deacetylases. However, unlike the SIN3 gene of Saccharomyces cerevisiae, pst1 + is essential for cell viability. Immunofluorescence microscopy indicated that Pst1p was localized in the nucleus. Consistent with the critical role previously reported for Sin3 proteins in the histone acetylation process, we found that the growth of the strain with thepst1-1 allele was supersensitive to the specific histone deacetylase inhibitor trichostatin A. However, our analysis of strains with the pst1-1 mutation was unable to detect any changes in the acetylation of specific lysines of histones H3 and H4 as measured in bulk chromatin. Interestingly, the pst1-1mutant strain produced wild-type levels of Tf1-encoded proteins and cDNA, indicating that the defect in transposition occurred after reverse transcription. The results of immunofluorescence microscopy showed that the nuclear localization of the Tf1 capsid protein was disrupted in the strain with the pst1-1mutation, indicating an important role of pst1 +in modulating the nuclear import of Tf1 virus-like particles.
15-712 Project Proposal

In virtually all scientific disciplines, technological advances over the past years and decades have resulted in an exponential growth in the quantity of raw scientific data available for analysis. Massive datasets, ranging from hundreds of MBs to many TBs, are increasingly common and available to the public. Spanning the breadth of scientific fields, this publicly accessible information includes NASA astrophysics and astronomy collections [1], partial three-dimensional mappings of the universe [2], earthquake and seismic data [3], complete genomes for a multitude of organisms [4], and so on. However, collecting and publishing raw data is only the beginning of scientific understanding. Unfortunately, the enormous benefits to be gained by thoroughly analyzing these datasets is typically matched by the complexity of such analysis. For instance, sequence alignment is a powerful technique for predicting the function of newly discovered genes [5], but computational limitations prevent the best algorithms available from being used on full datasets. Supercomputers and customized high-performance solutions such as the CLC Bioinformatics Cube [6] can sometimes employed, but the cost of such solutions is prohibitive. Furthermore, for some classes of scientific problems involving huge datasets (including those mentioned above), processing power can be largely wasted even on a supercomputer if the computation is disk-bound. With the advent of multi-core personal computers, clusters of commodity machines have the potential to become a reasonable alternative platform for intense scientific computing. Using clusters of readily available machines in place of supercomputers or problem-specific high-performance machines could not only reduce costs, power consumption, and possibly execution time, but it would also open the multitude of rich, massive datasets to a wider community of researchers, conceivably accelerating the rate of scientific discovery.
Auditory Induced Bounce Perception Persists as the Probability of a Motion Reversal is Reduced

When two identical targets move toward one another from opposite sides of a display and continue past one another along collinear trajectories, they can be perceived to either stream past or bounce off of one another. Streaming is the dominant perception in motion displays free of additional transients, while bouncing predominates when a transient (eg auditory or visual) is presented at the point of coincidence. We investigated whether the auditory induced bias towards bouncing would persist as the probability of a motion reversal was reduced by introducing a spatial offset either vertically in a 2-D display or in depth in a 3-D display. Offset conditions were combined with two auditory conditions (tone or no-tone at the point of coincidence) in the presence or absence of a central occluder. In conditions with no sound, streaming was reported on a clear majority of trials, regardless of spatial offset. When a transient tone was presented, reported motion reversals dominated and persisted for increasing verbal offsets up to 17.9 min of arc and for 3-D trajectory offsets up to 25.6 min of arc. The bounce-promoting effect of an auditory tone at the point of coincidence in stream/bounce displays persists in spite of rendering the visual motion sequence unambiguous and more consistent with streaming.