Miracle-dz/UniFAR-FTUs huggingface dataset:
Apoptosis-inducing antitumor efficacy of hexokinase II inhibitor in hepatocellular carcinoma

Hypoxia stimulates hepatocellular carcinoma (HCC) cell growth via hexokinase (HK) II induction, and alternatively, HK II inhibition induces apoptosis by activating mitochondrial signaling. This study was to investigate whether the induction of HK II by hypoxia is associated with enhanced mitochondrial stability and to confirm the apoptosis-inducing efficacy of HK II inhibitor in an in vivo model of HCC. Mitochondrial stability was examined by treating isolated mitochondria with deoxycholate, a permeability-enhancing agent. Alteration of permeability transition pore complex composition was analyzed by immunoprecipitation and immunoblotting. An in vivo model of HCC was established in C3H mice i.d. implanted with MH134 cells. The antitumor efficacy of i.p. given 3-bromopyruvate (3-BrPA), a HK II inhibitor, was evaluated by measuring tumor volumes and quantifying apoptosis using terminal deoxynucleotidyl transferase–mediated dUTP nick end labeling staining and 99mTc-hydrazinonicotinamide-Annexin V scans. Hypoxia enhanced mitochondrial stability, and this was inhibited by 3-BrPA treatment. In particular, HK II levels in permeability transition pore complex immunoprecipitates were reduced after 3-BrPA treatment. In mice treated with 3-BrPA, mean tumor volumes and tumor volume growth were found to be significantly reduced. Moreover, percentages of terminal deoxynucleotidyl transferase–mediated dUTP nick end labeling–positive cells were significantly increased in 3-BrPA–treated mice, and this apoptosis-inducing efficacy was reflected in vivo by 99mTc-hydrazinonicotinamide-Annexin V imaging. Our results show that hypoxia enhances mitochondrial stability via HK II induction and that HK II inhibitor treatment exhibits an in vivo antitumor effect by inducing apoptosis. Therefore, HK II inhibitors may be therapeutically useful for the treatment of advanced infiltrative hypovascular HCCs, which are growing in a hypoxic environment. [Mol Cancer Ther 2007;6(9):2554–62]
VLSI Implementation of a Cost-Efficient Near-Lossless CFA Image Compressor for Wireless Capsule Endoscopy

In this paper, a novel near-lossless color filter array (CFA) image compression algorithm based on JPEG-LS is proposed for VLSI implementation. It consists of a pixel restoration, a prediction, a run mode, and entropy coding modules. According to the information of the previous research, a context table and row memory consumed more than 81% hardware cost in a JPEG-LS encoder design. Hence, in this paper, a novel context-free and near-lossless image compression algorithm is presented. Since removing the context model causes decreasing of the compression performance, a novel prediction, run mode, and modified Golomb–Rice coding techniques were used to improve the compression efficiency. The VLSI architecture of the proposed image compressor consists of a register bank, a pixel restoration module, a predictor, a run mode module, and an entropy encoder. A pipeline technique was used to improve the performance of this. It contains only 10.9k gate count, and the core area is 30 $625~\mu \text{m}^{2}$ , synthesized by using a 90-nm CMOS process. Compared with the previous JPEG-LS designs, this paper reduces the gate counts by 44.1% and 41.7%, respectively, for five standard and eight endoscopy testing images in CFA format. It also improves the average PSNR values by 0.96 and 0.43 dB, respectively, for the same test images.
Evaluating the performance of Australian and New Zealand intensive care units in 2009 and 2010

The Australian and New Zealand Intensive Care Society Adult Patient Database (ANZICS APD) is one of the largest databases of its kind in the world and collects individual admissions' data from intensive care units (ICUs) around Australia and New Zealand. Use of this database for monitoring and comparing the performance of ICUs, quantified by the standardised mortality ratio, poses several theoretical and computational challenges, which are addressed in this paper. In particular, the expected number of deaths must be appropriately estimated, the ICU casemix adjustment must be adequate, statistical variation must be fully accounted for, and appropriate adjustment for multiple comparisons must be made. Typically, one or more of these issues have been neglected in ICU comparison studies. Our approach to the analysis proceeds by fitting a random coefficient hierarchical logistic regression model for the inhospital death of each patient, with patients clustered within ICUs. We anticipate the majority of ICUs will be estimated as performing ‘usually’ after adjusting for important clinical covariates. We take as a starting point the ideas in Ohlssen et al and estimate an appropriate null model that we expect these ICUs to follow, taking a frequentist rather than a Bayesian approach. This methodology allows us to rigorously account for the aforementioned statistical issues and to determine if there are any ICUs contributing to the Australian and New Zealand Intensive Care Society database that have comparatively unusual performance. In addition to investigating the yearly performance of the ICUs, we also estimate changes in individual ICU performance between 2009 and 2010 by adjusting for regression‐to‐the‐mean. Copyright © 2013 John Wiley & Sons, Ltd.
Expression of RoTat 1.2 Cross‐reactive Variable Antigen Type in Trypanosoma evansi and T. equiperdum

Abstract: The variable antigen type (VAT) RoTat 1.2 has been cloned from a T. evansi strain, isolated in 1982 from a water buffalo in Indonesia. All T. evansi isolates hitherto tested express this VAT. In a study on the differential diagnosis of T. equiperdum and T. evansi in horses, we investigated serological evidence for the expression of RoTat 1.2 in 11 T. evansi and six T. equiperdum populations originating from Asia, Europe, Africa, and the Americas. Preinfection sera and sera of days 7, 14, 25, and 35 post‐infection (p.i.) were analyzed for the presence of antibodies reactive with RoTat 1.2 in immune trypanolysis, ELISA/T. evansi and CATT/T. evansi. Within the duration of the experiment, all rabbits infected with T. evansi became positive in the three serological tests. Five out of six rabbits infected with T. equiperdum also became positive in the three tests. Only one T. equiperdum strain (the OVI strain from South Africa) did not induce the production of antibodies reactive with RoTat 1.2 and thus might not contain or express a VSG that shares epitopes similar to those on the RoTat 1.2 VSG. The data lead to the conclusion that T. equiperdum can express VSGs containing epitopes serologically similar to those in the T. evansi RoTat 1.2 VAT. This explains, in part, why the antibody detection tests based on Ro Tat 1.2 VSG cannot reliably distinguish between the infections caused by T. evansi and those caused by T. equiperdum. There are no data that contradict the possibility that the putative T. equiperdum strains, which express VSGs with epitopes similar to those on RoTat 1.2, are actually T. evansi.
Analysis of the type material of Pinnularia divergentissima (Grunow in Van Heurck) cleVe (Bacillariophyceae)

The analysis of the type material of Pinnularia divergentissima (Grunow in Van Heurck) Cleve revealed the presence of two distinct Pinnularia taxa in the same slide. Comparison with the original drawing of P. divergentissima by Grunow showed that recent taxonomic treatments of P. divergentissima are not in accordance with the original diagnosis. Both species in the type material are morphologically characterized and the correct identity of P. divergentissima is established whereas the second taxon is described as P. pseudodivergentissima sp. nov. Additionally, the type material of P. fottii J.Bilý et Marvan and P. martinii Krasske is likewise analysed and both taxa are separated from P. divergentissima. Finally, the morphological analysis of a fifth taxon from the sub-Antarctic Region resulted in the description of a new taxon, P. lindanedbalovae Van de Vijver et Moravcova sp. nov.
Faster Protein Splicing with the Nostoc punctiforme DnaE Intein Using Non-native Extein Residues

Background: Inteins are protein maturation machines that enable technologies for regulating enzymes and protein semisynthesis. Results: Robust splicing was achieved with novel genetically selected exteins. Conclusion: In contrast to commonly held perceptions, the natural extein was not the fastest splicing substrate. Significance: Natural precursors balance extein- and intein-selective pressures. Specificity studies provide a predictive rubric for identifying new intein insertion sites. Inteins are naturally occurring intervening sequences that catalyze a protein splicing reaction resulting in intein excision and concatenation of the flanking polypeptides (exteins) with a native peptide bond. Inteins display a diversity of catalytic mechanisms within a highly conserved fold that is shared with hedgehog autoprocessing proteins. The unusual chemistry of inteins has afforded powerful biotechnology tools for controlling enzyme function upon splicing and allowing peptides of different origins to be coupled in a specific, time-defined manner. The extein sequences immediately flanking the intein affect splicing and can be defined as the intein substrate. Because of the enormous potential complexity of all possible flanking sequences, studying intein substrate specificity has been difficult. Therefore, we developed a genetic selection for splicing-dependent kanamycin resistance with no significant bias when six amino acids that immediately flanked the intein insertion site were randomized. We applied this selection to examine the sequence space of residues flanking the Nostoc punctiforme Npu DnaE intein and found that this intein efficiently splices a much wider range of sequences than previously thought, with little N-extein specificity and only two important C-extein positions. The novel selected extein sequences were sufficient to promote splicing in three unrelated proteins, confirming the generalizable nature of the specificity data and defining new potential insertion sites for any target. Kinetic analysis showed splicing rates with the selected exteins that were as fast or faster than the native extein, refuting past assumptions that the naturally selected flanking extein sequences are optimal for splicing.
A Highly Parallel and Scalable CABAC Decoder for Next Generation Video Coding

Future video decoders will need to support high resolutions such as Quad Full HD (QFHD, 4096 × 2160) and fast frame rates (e.g., 120 fps). Many of these decoders will also reside in portable devices. Parallel processing can be used to increase the throughput for higher performance (i.e., processing speed), which can be traded-off for lower power with voltage scaling. The next generation standard called High Efficiency Video Coding (HEVC), which is being developed as a successor to H.264/AVC, not only seeks to improve the coding efficiency but also to account for implementation complexity and leverage parallelism to meet future power and performance demands. This paper presents a silicon prototype for a pre-standard algorithm developed for HEVC (“H.265”) called Massively Parallel CABAC (MP-CABAC) that addresses a key video decoder bottleneck. A scalable test chip is implemented in 65-nm and achieves a throughput of 24.11 bins/cycle, which enables it to decode the max H.264/AVC bit-rate (300 Mb/s) with only a 18 MHz clock at 0.7 V, while consuming 12.3 pJ/bin. At 1.0 V, it decodes a peak of 3026 Mbins/s for a bit-rate of 2.3 Gb/s, enough for QFHD at 186 fps. Both architecture and joint algorithm-architecture optimizations used to reduce critical path delay, area cost and memory size are discussed.
Enzyme Function Classification Using Protein Sequence Features and Random Forest

Enzymes are proteins that catalyze bio-chemical reactions in different ways and play important roles in metabolic pathways. The exponential rise in sequences of new enzymes has necessitated developing methods that accurately predict their function. To address this problem, approaches that cluster enzymes based on their sequence and structural similarity have been applied, but are known to fail for dissimilar proteins that perform the same function. In this paper, we present a machine learning approach to accurately predict the main function class of enzymes based on a unique set of 73 sequence-derived features. Our features can be extracted using freely available online tools. We used different multi-class classifiers to categorize enzyme protein sequences into one of the NC-IUBMB defined six main function classes. Amongst the classifiers, Random Forest reported the best results with an overall accuracy of 88% and precision and recall in the range of 84% to 93% and 82% to 93% respectively. Our results compare favorably with existing methods, and in some cases report better performance. Random Forest has been proven to be a very efficient data mining algorithm. This paper is first in exploring their application to enzyme function prediction. The datasets can be accessed online at the location: http://cholera.ece. northwestern.edu/EnzyPredict.
Delayed mating in tortricid leafroller species: simultaneously aging both sexes prior to mating is more detrimental to female reproductive potential than aging either sex alone

Abstract The effect of delayed mating on reproductive potential, longevity and oviposition period of female redbanded leafroller, Argyrotaenia velutinana (Walker) and Pandemis leafroller, Pandemis pyrusana Kearfott, was investigated in the laboratory. Virgin female or male moths of each species were held for 1, 2, 4, 6 or 10 days prior to pairing with one-day-old virgin conspecifics of the opposite sex. In addition, reproductive potential was assessed when both sexes of each species were aged for those periods prior to pairing. The expected reproduction of female A. velutinana was reduced by 34, 53, 71 and 81% for 2, 4, 6 and 10-day delays in female mating, respectively. For P. pyrusana, expected reproduction was reduced by 47, 74, 85 and 93% for 2, 4, 6 and 10-day delays in female mating, respectively. Increasing male age at mating in both species had a lesser effect on female reproductive output compared with increasing female age at mating. As male A. velutinana age at mating increased, the expected reproduction of female A. velutinana was reduced by 15, 45, 54 and 70% for 2, 4, 6 and 10-day delays, respectively. Comparing male P. pyrusana of various ages at mating, expected reproduction was reduced by 14, 42, 64 and 79% for 2, 4, 6 and 10-day delays in mating, respectively. The decrease in female reproduction when both sexes were aged prior to mating was higher than when either sex alone was aged prior to pairing with a one-day-old virgin of the opposite sex. The expected reproduction of female A. velutinana was reduced by 60, 83, 96 and 98% for 2, 4, 6 and 10-day delays in mating of both sexes, respectively. Only 7.5% of female eggs hatched when both sexes of A. velutinana were aged ten days prior to mating. When simultaneously aging both sexes of P. pyrusana prior to mating, expected reproduction was reduced by 71, 93, 96 and 99% for 2, 4, 6 and 10-day delays in mating, respectively. No P. pyrusana eggs hatched after a ten-day delay of mating for both sexes. For both species, female longevity increased and duration of oviposition period decreased with increasing female age at mating. Our results demonstrate that delayed mating in both females and males negatively affects female reproductive output in both species and that simultaneous aging of both sexes prior to mating has a greater effect than aging either sex alone. Our results suggest that laboratory studies that have paired aged females or aged males with conspecifics of optimal reproductive maturity have likely underestimated the effects of delayed mating on reproductive output.
Northeastern extension of Neogene magmatism in Africa: Evidence from the Zitouna rhyolite, Algeria

espanolLa riolita de Zitouna es la representacion mas oriental del magmatismo neogeno en el noreste de Argelia. Esta formada por dos cuerpos intrusivos rioliticos: el primer afloramiento es vagamente conocido y no ha sido datado; el segundo es de mayores dimensiones y no ha sido descrito previamente. Se trata de una roca bien diferenciada que no excede de los 12 Ma (Post-Serravaliense). Los datos geoquimicos muestran que corresponde a un granito de tipo S con alto caracter peraluminico, lo que corrobora un protolito cortical. La riolita de Zitouna es considerada como la continuacion de otros episodios magmaticos vecinos y puede ser relacionada con la evolucion tectono-magmatica del noreste africano durante el Neogeno superior. EnglishThe Zitouna rhyolite is the easternmost representative of the Neogene magmatism in the Northeast of Algeria. It is composed of two intrusive rhyolitic apexes: the first outcrop is poorly known and not dated; the second one is greater, and not previously described. It is a well-differentiated rock that does not exceed 12 Ma (Post-Serravallian). Geochemical data show that it belongs to S-type granites with a high peraluminous character corroborating a crustal protolith. The Zitouna rhyolite is considered as the continuation of other neighbouring magmatic episodes and can be related to the late Neogene tectono-magmatic evolution of northeast Africa.Keywords: rhyolite, post-Serravallian, S-type granites, peraluminous, Zitouna, Algeria.
miRNA-411 acts as a potential tumor suppressor miRNA via the downregulation of specificity protein 1 in breast cancer

The expression and functions of microRNA (miR)-411 have been investigated in several types of cancer. However, until now, miR-411 in human breast cancer has not been examined. The present study investigated the expression, biological functions and molecular mechanisms of miR-411 in human breast cancer, discussing whether it offers potential as a therapeutic biomarker for breast cancer in the future. The expression levels of miR-411 in human breast cancer tissues and cells were measured using reverse transcription-quantitative polymerase chain reaction analysis. Following transfection with miR-411 mimics, an MTT assay, cell migration and invasion assay, western blot analysis and luciferase assay were performed in human breast cancer cell lines. According to the results, it was found that miR-411 was significantly downregulated in breast cancer, and associated with lymph node metastasis and histological grade. Additionally, it was observed that miR-411 suppressed cell growth, migration and invasion in the breast cancer cells. The present study also provided the first evidence, to the best of our knowledge, that miR-411 was likely to directly target specificity protein 1 in breast cancer. These findings indicated that miR-411 may be used a therapeutic biomarker for the treatment of breast cancer in the future.
Evaluation of Occupational Exposure of Shoe Makers to Benzene and Toluene Compounds in Shoe Manufacturing Workshops in East Tehran

Background Shoe making is among the oldest traditional occupations. Hazardous chemical substances such as adhesives containing benzene and toluene are used in the manufacturing process. Due to the lack of studies on exposure of shoemakers to benzene and toluene in Iran, this study was organized aiming at evaluating occupational exposure and risk assessment in shoemakers. Materials and Methods Overall, 48 shoemakers (12 workshops) in East Tehran were selected randomly for this study. Personal exposure of shoemakers in four different task groups of cutting, modeling, fitting and finishing was examined during three consecutive months (October, November and December) with different climatic conditions. Sampling and analysis of samples were based on an OSHA method (Method No.12). Results The results of personal monitoring of subjects’ exposure to benzene and toluene in each of the three consecutive months (Mean ± standard error) were 1.10± 0.11, 1.37 ± 0.14 and 1.52 ± 0.18ppm, 11.78 ± 1.77, 14.87 ± 1.71 and 16.08 ± 2.31ppm respectively. Due to climatic temperature changes from October to December and restriction of air flow due to closure of windows and shut down of general ventilation systems, a general trend of increased exposure was noticed. However, the difference among these three examinations was not statistically significant. Shoemakers in four task groups did not have statistically significant differences in exposure to benzene and toluene. The severity of shoemaker's exposure to toluene was significantly correlated with the number of manufactured shoes and the amount of glue used for the process. Conclusion Considering the magnitude of personal exposure of task groups to benzene and toluene which was higher than TLV-TWA and unacceptably high risk of cancer and non-cancerous diseases in these subjects, improvement of work conditions for shoemakers seems imperative.
Estimation of microbial nitrogen in nylon-bag residues by feed 15N dilution

1. Rapeseed (Brussicu nupus), barley grain, ryegrass (Loliurnperenne) and barley straw were labelled with 15N as an internal marker. The dilution of 15N was used to estimate microbial N (RMN15N) in the feed residues in nylon bags incubated in the rumen for 5, 12 and 24 h. For comparative purposes, diaminopimelic acid (DAP) content of the residues was also determined and rumen microbial N (RMNDAP-N) in the feed residues calculated using DAP as a bacterial marker. The influence of two bag pore sizes (20 μm and 40 μm) with different sample sizes (1 g and 5 g respectively) was also studied. 2. For all feeds, the average disappearance of 15N was faster than that of total N, the difference between N and 15N disappearance being marked with barley, ryegrass and barley straw. The disappearance of microbially corrected dry matter (DM; correction calculated from the 15N values) was, accordingly, always faster than the uncorrected DM disappearance. Except for the bag pore/sample size effect for N disappearance, significant (P < 0.01–0.001) feed, pore/sample size and incubation-time effects were always found for the disappearance values. 3. Errors (%) resulting from the microbial contamination (calculated from the 15N values) in N-loss measurement with rapeseed, barley, ryegrass and barley straw, at 5, 12 and 24 h in 20 μm bags were respectively: –1.8, –3.9, –0.9; –3.8, –22.4, –3.8; –7.2, –4.1, –2.9; –164.5, –146.3, –204.6. In 40 μm bags the corresponding errors were respectively: –4.4, –1.2, –0.7; –26.1, –10.5, –3.9; –13.2, –6.4, –5.5; –221.2, –310.1, –1284.6. 4. The largest residual proportions of RMN15N, RMNDAP-N and DAP-N (% of total N) were found in barley straw, followed by barley, ryegrass and rapeseed, in that order. RMN15N (g/kg residual DM) followed the descending order: barley, ryegrass, straw, rapeseed. RMNDAP-N, (g/kg residual DM) and DAP (mg/kg residual DM) followed the descending order: barley, ryegrass, rapeseed and barley straw. Feed, pore/sample size and incubation-time effects were always significant (P < 0.001). 5. With 40 μm bags RMN15N values of barley, ryegrass and barley straw (expressed as % of total N or g/kg residual DM) were substantially higher than those of RMNDAP-N With 20 μm bags the RMN15N and RMNDAP-N values were generally quite close for these feeds. With rapeseed residues, RMN15N was clearly lower than RMNDAP-N with 20 μm bags, but only small differences were found with 40 μm bags. 6. A more diverse microbial colonization of feed samples was indicated in the 40 μm bags compared with the 20 μm bags. It was also noticed, consequently, that in most cases larger error resulted from the microbial contamination in 40 μm bags.