Miracle-dz/UniFAR-FTUs huggingface dataset:
bcl-2 gene hypomethylation and high-level expression in B-cell chronic lymphocytic leukemia.

The bcl-2 gene becomes transcriptionally deregulated in the majority of low-grade non-Hodgkin lymphomas as a result of t(14;18) translocations that place the bcl-2 gene at 18q21 into juxtaposition with the Ig heavy-chain locus at 14q32. This chromosomal translocation or similar bcl-2 gene rearrangements involving the Ig light-chain genes have been reported to occur in some cases of B-cell chronic lymphocytic leukemia (B-CLL). We analyzed the structure, methylation, and expression of the bcl-2 gene in 20 cases of B-CLL or closely related variants of this lymphoproliferative disorder, including at least 16 typical examples of CD5+ B-CLL. None of the 20 specimens had evidence of bcl-2 gene rearrangements, based on Southern blot analysis using three different bcl-2 probes. However, immunoblot analysis using antibodies specific for the Bcl-2 protein showed that 14 of 20 cases (70%) contained levels of p26-Bcl-2 that were equal to or greater than those found in a t(14;18)-bearing lymphoma cell line. Furthermore, in 19 of 20 cases (95%), the Bcl-2 protein was present at levels that were 1.7- to 25-fold higher than in normal peripheral blood lymphocytes. These differences in the relative levels of Bcl-2 protein among cases of B-CLL appeared to be functionally significant, in that a preliminary analysis of 3 representative cases showed that CLL cells with higher levels of Bcl-2 protein survived longer in culture and were delayed in their onset of DNA degradation relative to CLL cells with lower Bcl-2 protein levels. Evaluation of the methylation status of the bcl-2 gene using the isoschizomers Msp I and Hpa II, and a probe corresponding to the first major exon of the gene showed complete demethylation of both copies of the bcl-2 gene in a region corresponding to a 2.4-kb Msp I fragment in all 20 cases of B-CLL. In contrast, analysis of 6 of 6 B-cell lines that harbor a t(14;18) was consistent with hypomethylation of only one of the two bcl-2 alleles. Neither copy of the bcl-2 gene was demethylated in this region in 5 of 5 lymphoid cell lines that lack this translocation. However, hypomethylation of the bcl-2 gene did not necessarily correlate with the relative levels of Bcl-2 protein present in the B-CLL cells, suggesting that additional mechanisms for regulating bcl-2 expression are involved. (ABSTRACT TRUNCATED AT 400 WORDS)
Azithromycin, fluoroquinolone and chloramphenicol resistance of non-chlamydia conjunctival bacteria in rural community of Ethiopia

Aim: To determine profiles of non-chlamydia conjunctival bacteria and their antimicrobial susceptibility from adults who underwent trachomatous trichiasis surgery in rural areas of Ethiopia. Materials and Methods: A cross-sectional study was conducted in rural districts in West Gojjam administrative zone. Conjunctival swabs were collected during surgery and transported using Stuart transport broth (Oxoid, UK). Antibiotic susceptibility of conjunctival isolates was determined using the Kirby-Bauer disc-diffusion method. Results: Non-chlamydia pathogenic bacteria were recovered from conjunctiva of 438 (31%) participants before treatment. The isolated conjunctival bacteria were Staphylococcus aureus, coagulase-negative Staphylococci, Streptococcus group (A, C, F and G), Enterococci, Streptococcus pneumoniae, Moraxella spp. , Escherichia coli, Citrobacter spp. , Proteus spp. , Klebsiella spp. , Pseudomonas spp. and Enterobacter spp. Overall, resistance rates of 57.8% to azithromycin and 68.5% to chloramphenicol were found. However, 86-94.4% sensitivity was demonstrated to ciprofloxacin and norfloxacin. Moderate sensitivity rates (61.8-78.4%) were observed to ceftriaxone, tetracycline and cotrimoxazole. Conclusion: Fluoroquinolones that have activity against the majority of bacterial isolates were potent at in vitro. However, unacceptably high levels of resistance to azithromycin and chloramphenicol in rural community indicated a need for further study and antimicrobial resistance surveillance.
Expression of CD44 3′-untranslated region regulates endogenous microRNA functions in tumorigenesis and angiogenesis

The non-coding 3′-untranslated region (UTR) plays an important role in the regulation of microRNA (miRNA) functions, since it can bind and inactivate multiple miRNAs. Here, we show the 3′-UTR of CD44 is able to antagonize cytoplasmic miRNAs, and result in the increased translation of CD44 and downstream target mRNA, CDC42. A series of cell function assays in the human breast cancer cell line, MT-1, have shown that the CD44 3′-UTR inhibits proliferation, colony formation and tumor growth. Furthermore, it modulated endothelial cell activities, favored angiogenesis, induced tumor cell apoptosis and increased sensitivity to Docetaxel. These results are due to the interaction of the CD44 3′-UTR with multiple miRNAs. Computational algorithms have predicted three miRNAs, miR-216a, miR-330 and miR-608, can bind to both the CD44 and CDC42 3′-UTRs. This was confirmed with luciferase assays, western blotting and immunohistochemical staining and correlated with a series of siRNA assays. Thus, the non-coding CD44 3′-UTR serves as a competitor for miRNA binding and subsequently inactivates miRNA functions, by freeing the target mRNAs from being repressed.
FIVE‐AMINOLEVULINIC ACID FOR FLUORESCENCE‐GUIDED RESECTION OF RECURRENT MALIGNANT GLIOMAS: A PHASE II STUDY

OBJECTIVETo assess the feasibility of 5-aminolevulinic acid (5-ALA) fluorescence guidance for resection of recurrent malignant brain tumors. METHODSIn a multicenter prospective, single-arm, uncontrolled phase II study, 36 patients with recurrent glioma (World Health Organization grade III/IV) received 5-ALA before surgery. After microsurgical resection, biopsies from pathological and nonpathological areas (as identified under conventional white light) were obtained to determine the positive predictive value (PPV) of 5-ALA–induced tissue fluorescence in detecting tumors. Adverse events, neurological examinations, and survival data were documented for a minimal follow-up of 6 months. RESULTSThe patient-based PPV, defined as the percentage of patients showing positive tumor cell identification in all biopsies taken from areas of weak and strong fluorescence was 97.2% for pathological areas and 79.4% in nonpathological areas. Within areas of strong fluorescence, PPV was higher (91.7%) compared with that of weak fluorescence (82.4%). On the biopsy level for nonpathological-appearing tissue under white light (157 biopsies), the PPV of tissue fluorescence was 93.0% compared with 99.5% in pathological-appearing tissue (197 biopsies). Again, within areas of strong fluorescence, PPV was higher (96.9%) compared with that of weak fluorescence (90.3%). There were no adverse events pertaining to the study drug. CONCLUSION5-ALA fluorescence has a high predictive value for the detection of tumor in recurrent gliomas. Prior treatment modalities, such as radiation or chemotherapy, do not invalidate the fluorescence guidance with 5-ALA. 5-ALA fluorescence guidance is an effective surgical adjunct in the surgery of recurrent malignant gliomas.
Potentials on Large Spacecraft in LEO

A system-oriented computer code is used to predict surface charging due to voltages generated within a satellite operating in the typical dense plasma environment of LEO. The use of this code is demonstrated by predicting the expansion of electric fields onto a kapton surface from a pinhole over a biased conductor in a LEO environment. The results are compared to a more-exact solution and experimental data.
Domain-Independent Unsupervised Text Segmentation for Data Management

In this study, we have proposed a domain-independent unsupervised text segmentation method, which is applicable to even if unseen single document. This proposed method segments text documents by evaluating similarity between sentences. It is generally difficult to calculate semantic similarity between words that comprise sentences when the domain knowledge is insufficient. This problem influences segmentation accuracy. To address this problem, we use word 2 vec to calculate semantic similarity between words. Using word 2 vec, we embed semantic relationships between words in a vector space by training with large domain-independent corpora. Furthermore, we combine semantic and collocation similarities, i.e., The features between words within a document. The proposed method applies this combined similarity to affinity propagation clustering. Similarity between sentences is defined based on the earth mover's distance between the frequencies of the obtained topical clusters. After calculating similarity between sentences, segmentation boundaries are automatically optimized using dynamic programming. The experimental results obtained using two datasets show that the proposed method clearly outperforms state-of-the-art domain-independent approaches and obtains equal performance with state-of-the-art domain-dependent approaches such as those that use topic modeling.
Physico-chemical properties and DPPH-ABTS scavenging activity of some local pomegranate (Punica granatum) ecotypes

Peels and fresh pomegranate extracts were used in the present study for the determination of the physic-chemical properties and DPPH-ABTS scavenging activities. Total sugars of juice are fructose (ca. 7 g/100 ml) and glucose (ca. 8 g/100 ml). Contents of soluble proteins in juice extracts are about 7 g/l (Bradford assays) and 22% (Kjeldhal assays) from dry pulp. Minerals in peel and juice are respectively 9.43±0.93 and 9.46±1.05 mg/100 ml for posphorus and 210.86±10.70 and 271.94±60.59 mg/100 g for potassium. The sodium contents are nearly 7 mg/100 ml in both peel and juice. Highly antioxidant contents in peels were confirmed. Free radical scavenging is about 3.58±0.38 µg/ml in peel. The antioxidant capacity value determined by ABTS was 7.364±0.403 mM Trolox equivalent antioxidant capacity/100 g dry weight. These findings implied that bio-active compounds from the peel might be potential resources for the development of antioxidant function dietary food.
Comparative evaluation of apical microleakage in immediate and delayed postspace preparation using four different root canal sealers: An in vitro study

Background: Endodontically treated teeth often lack sufficient support for a permanent restoration. During post space preparation, it is important not to disturb the integrity of the apical seal. Aim: This study compared the effect of immediate versus delayed post space preparation on the apical seal using four different sealers. Materials and Methods: One hundred and thirty single rooted teeth were biomechanically prepared and obturated with single cone gutta-percha and 4 sealers: Endoflas FS, AH Plus, Gutta flow and MTA. Teeth were divided randomly into eight groups, post spaces were prepared using Gates Glidden drills immediately for group I, III, IV and VII. For groups II, IV, VI and VIII prepared after storage of the specimens in 100% humidity for one week. The samples were kept in methylene blue dye, centrifuged at 3000 rpm for 3 min sectioned and then measured under stereomicroscope for apical leakage. Statistical Analysis: The data was analysed using one way ANOVA and post hoc Tukey test. Results: All the specimens showed dye leakage, and a statistically significant difference was seen among all the groups (P > 0.05) except Gutta flow. Conclusion: Less leakage is seen when post space is prepared immediately.
Three-dimensional molecular dynamics analysis of processing using a pin tool on the atomic scale

A three-dimensional model of molecular dynamics (MD) is proposed to study the effects of tool geometry and processing resistance on the atomic-scale cutting mechanism. The model includes the utilization of the Morse potential function to simulate the interatomic force between the workpiece and a tool. The results show that the cutting resistance increases with the angle of the pin tool and the depth of cut, and the cutting force is essentially constant over the range of velocities simulated. In addition, the obtained cutting resistance of present MD simulation exhibits an evident relationship to the ratio of the vertical and the horizontal contact area between the tool and the workpiece within the range of a pin angle of 90-150°. Finally, work hardening and stick-slip phenomena during the process are also observed.
Immediate Effect of Acupuncture on the Sleep Pattern of Patients with Obstructive Sleep Apnoea

Background Most patients with obstructive sleep apnoea (OSA) do not tolerate treatment with nasal continuous positive airway pressure, the ‘gold standard’ treatment for this condition. It was shown in a pilot study that acupuncture was more effective than placebo treatment (sham acupuncture) in producing significant changes in the respiratory events assessed by polysomnography (PSG). Objectives To investigate the immediate effect of manual acupuncture (MA) and electroacupuncture (EA) on the sleep pattern of patients presenting with moderate OSA. Methods 40 patients with an Apnoea–Hypopnoea Index (AHI) of 15–30/h were randomly allocated to MA treatment (n=10), EA 10 Hz treatment (n=10), EA 2 Hz treatment (n=10) and a no-treatment control group (n=10). The patients received MA or EA (2 or 10 Hz) just before the PSG study at 20:00. Results The AHI (p=0.005; p=0.005), the Apnoea Index (p=0.038; p=0.009) and the respiratory events (p=0.039; p=0.014) decreased significantly in the MA and EA 10 Hz groups, respectively (AHI (21.9, 11.2), Apnoea Index (5.15, 0.7), respiratory events (120.5, 61.0) in the MA group before and after. AHI (20.6, 9.9), Apnoea Index (8.2, 0.3), respiratory events (117.0, 56.0) in the EA 10 Hz group before and after). The micro-arousals decreased only in the MA group (146.0 vs 88.5, p=0.0002). There were no significant changes in the EA 2 Hz group or in the control group. Conclusion A single session of either MA or EA 10 Hz had an acute effect in reducing the AHI as well as the number of nocturnal respiratory events of patients presenting with moderate OSA.
Effects of ligand distribution on receptor-diffusion-mediated cellular uptake of nanoparticles

Biophysical-factor-dependent cellular uptake of nanoparticles (NPs) through receptor-diffusion-mediated endocytosis bears significance in pathology, cellular immunity and drug-delivery systems. Advanced nanotechnology of NP synthesis provides methods for modifying NP surface with different ligand distributions. However, no report discusses effects of ligand distribution on NP surface on receptor-diffusion-mediated cellular uptake. In this article, we used a statistical dynamics model of receptor-diffusion-mediated endocytosis to examine ligand-distribution-dependent cellular uptake dynamics by considering that ligand–receptor complexes drive engulfing to overcome resistance to membrane deformation and changes in configuration entropy of receptors. Results showed that cellular internalization of NPs strongly depended on ligand distribution and that cellular-uptake efficiency of NPs was high when ligand distribution was within a range around uniform distribution. This feature of endocytosis ensures robust infection ability of viruses to enter host cells. Interestingly, results also indicated that optimal ligand distribution associated with highest cellular-uptake efficiency slightly depends on distribution pattern of ligands and density of receptors, and the optimal distribution becomes uniform when receptor density is sufficiently large. Position of initial contact point is also a factor affecting dynamic wrapping. This study explains why most enveloped viruses present almost homogeneous ligand distribution and is useful in designing controlled-release drug-delivery systems.
A Multigraph Representation for Improved Unsupervised/Semi-supervised Learning of Human Actions

Graph-based methods are a useful class of methods for improving the performance of unsupervised and semi-supervised machine learning tasks, such as clustering or information retrieval. However, the performance of existing graph-based methods is highly dependent on how well the affinity graph reflects the original data structure. We propose that multimedia such as images or videos consist of multiple separate components, and therefore more than one graph is required to fully capture the relationship between them. Accordingly, we present a new spectral method - the Feature Grouped Spectral Multigraph (FGSM) - which comprises the following steps. First, mutually independent subsets of the original feature space are generated through feature clustering. Secondly, a separate graph is generated from each feature subset. Finally, a spectral embedding is calculated on each graph, and the embeddings are scaled/aggregated into a single representation. Using this representation, a variety of experiments are performed on three learning tasks - clustering, retrieval and recognition - on human action datasets, demonstrating considerably better performance than the state-of-the-art.
Sintering and mechanical properties of porcelains prepared from algerian raw materials

A porcelana e um tipo de cerâmica altamente valorizada pela sua beleza e resistencia mecânica. O objetivo geral deste trabalho e utilizar materias-primas locais nas seguintes fracoes: 37% em peso de caulim, feldspato 35% em peso e 28% em peso de quartzo. Esta composicao foi escolhida com base em diagramas de fase ternarios (caulim, feldspato-quartzo). O comportamento de densificacao indicou que amostras sinterizadas a 1200 °C por 2 h com taxa de aquecimento de 5 °C/min, tem uma densidade de cerca de 2,50 g/cm3. Este valor e ligeiramente superior ao relatado para os produtos de porcelana convencional (2,45 g/cm3). Especimes de porcelana, com e sem calcinacao sinterizadas a 1200 °C por 2 h tem valores de resistencia a tracao de cerca de 45 e 73 MPa, respectivamente (valores equivalentes de resistencia a flexao de aproximadamente 122 e 197 MPa, respectivamente). Os valores de resistencia a flexao de ambos os especimes sao muito superiores aos relatados para porcelanas convencionais (variou entre 60 e 80 MPa). Mais ainda, o valor da micro-dureza das amostras sem calcinacao a 1200 °C e de 9,3 ± 0,2 GPa que e maior do que os produtos comerciais de porcelana (5,5 GPa).
COEXISTENCE OF EVOLVING BACTERIA STABILIZED BY A SHARED BLACK QUEEN FUNCTION

The Black Queen Hypothesis (BQH) was originally proposed to explain the dependence of some marine bacteria on helper organisms for protection from hydrogen peroxide (HOOH). The BQH predicts that selection for the evolutionary loss of leaky functions from individuals can produce commensal or mutualistic interactions. We demonstrated the leakiness of HOOH detoxification by complementing a HOOH‐sensitive Escherichia coli mutant with a plasmid‐encoded HOOH‐detoxifying enzyme, KatG, and then evolving populations founded by this strain in two environments. When HOOH was absent, plasmid‐carrying cells were outcompeted by plasmid‐free segregants, reflecting the high cost of KatG expression. However, plasmid‐carrying and plasmid‐free cells coexisted for at least 1200 generations in three replicate populations evolved in the presence of HOOH, although their relative proportions fluctuated as beneficial mutations arose in one type or the other. Evolved plasmid‐bearing cells reduced the cost of plasmid carriage even as they increased the rate of HOOH removal relative to the ancestor. Meanwhile, plasmid‐free cells remained dependent on HOOH detoxification by the plasmid‐bearing cells. These results demonstrate that partitioning of a Black Queen function can enable the stable coexistence of very similar organisms, even in this most restrictive case where the two types are competing for a single resource.
PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains

Degenerate PCR primers, UP-1 and UP-2r, for the amplification of DNA gyrase subunit B genes (gyrB) were designed by using consensus amino acid sequences of gyrases from Escherichia coli, Pseudomonas putida, and Bacillus subtilis. In addition to the degenerate sequences, these primers have sequences at the 5' end which allow direct sequencing of amplified PCR products. With these primers, DNA segments of the predicted size were amplified from a variety of gram-negative and gram-positive genera. The nucleotide sequences of the amplified gyrB DNA from three P. putida strains were determined directly from the amplified fragments. The base substitution frequency of gyrB between the strains of P. putida was much higher than that of the 16S rRNA gene. With a specific set of PCR primers, it was possible to amplify gyrB fragments selectively from P. putida or its subgroups. The direct sequencing method of gyrB developed in this study provides a rapid and convenient system for bacterial identification, taxonomic analysis, and monitoring of bacteria in the natural environment.
Photoactivatable GFP resolves Drosophila mesoderm migration behaviour

Mesoderm migration is a pivotal event in the early embryonic development of animals. One of the best-studied examples occurs during Drosophila gastrulation. Here, mesodermal cells invaginate, undergo an epithelial-to-mesenchymal transition (EMT), and spread out dorsally over the inner surface of the ectoderm. Although several genes required for spreading have been identified, our inability to visualise mesodermal cells in living embryos has left us to speculate about the cell rearrangements involved. Several mechanisms, such as chemotaxis towards a dorsally expressed attractant, differential affinity between mesodermal cells and the ectoderm, and convergent extension, have been proposed. Here we resolve the behaviour of Drosophila mesodermal cells in live embryos using photoactivatable-GFP fused to α-Tubulin (PAGFP-Tub). By photoactivating presumptive mesodermal cells before gastrulation, we could observe their migration over non-fluorescent ectodermal cells. We show that the outermost (outer) cells, which are in contact with the ectoderm, migrate dorsolaterally as a group but can be overtaken by more internal (inner) cells. Using laser-photoactivation of individual cells, we then show that inner cells adjacent to the centre of the furrow migrate dorsolaterally away from the midline to reach dorsal positions, while cells at the centre of the furrow disperse randomly across the mesoderm, before intercalating with outer cells. These movements are dependent on the FGF receptor Heartless. The results indicate that chemotactic movement and differential affinity are the primary drivers of mesodermal cell spreading. These characterisations pave the way for a more detailed analysis of gene function during early mesoderm development.
Cancer-associated TERT promoter mutations abrogate telomerase silencing

Mutations in the human telomerase reverse transcriptase (TERT) promoter are the most frequent non-coding mutations in cancer, but their molecular mechanism in tumorigenesis has not been established. We used genome editing of human pluripotent stem cells with physiological telomerase expression to elucidate the mechanism by which these mutations contribute to human disease. Surprisingly, telomerase-expressing embryonic stem cells engineered to carry any of the three most frequent TERT promoter mutations showed only a modest increase in TERT transcription with no impact on telomerase activity. However, upon differentiation into somatic cells, which normally silence telomerase, cells with TERT promoter mutations failed to silence TERT expression, resulting in increased telomerase activity and aberrantly long telomeres. Thus, TERT promoter mutations are sufficient to overcome the proliferative barrier imposed by telomere shortening without additional tumor-selected mutations. These data establish that TERT promoter mutations can promote immortalization and tumorigenesis of incipient cancer cells. DOI: http://dx.doi. org/10.7554/eLife.07918. 001