Miracle-dz/UniFAR-FTUs huggingface dataset:
Two distinct subtypes of hepatitis C virus defined by antibodies directed to the putative core protein

Four distinct genotypes of hepatitis C virus types I, II, III and IV have been identified by comparison of nucleotide sequences of isolates from different areas of the world. We examined the possibility that hepatitis C virus may have serologically definable subtypes. Enzyme‐linked immunosorbent assay systems were prepared by use of two synthetic peptides deduced from the putative core protein of hepatitis C virus. The following are the two peptides that were used: (a) IPKARRPEGRTWAQPGY (subtype‐1) conserved in hepatitis C virus isolates with type I and type II genotypes; and (b) IPKDRRSTGKSWGKPGY (subtype‐2) conserved in type III and type IV genotypes. With the enzyme‐linked immunosorbent assays, the subtype‐1 antibodies were detected in 26 (68%) of 38 subjects whose hepatitis C virus RNA had been genotyped as type I or type II, whereas subtype‐2 antibodies were not detected. Inversely, the subtype‐2 antibodies were detected in 10 (56%) of 18 subjects with hepatitis C virus RNA genotypes III or IV, whereas subtype‐1 antibodies were detected in none of them. These results suggest that hepatitis C virus has two serologically distinguishable core antigen subtypes, corresponding to either genotype I/II or genotype III/IV. Subtyping of HCV by serological methods would contribute to tracking transmission routes of the virus, especially in cases where serum samples were not stored under conditions to preserve RNA or in infected hosts who have cleared the virus and therefore have only antibodies remaining to identify the infection. (HEPATOLOGY 1992;16:886–891.)
Near Shannon Limit Performance of Low Density Parity Check Codes

We report the empirical performance of Gallager’s low density parity check codes on Gaussian channels. We show that performance substantially better than that of standard convolutional and concatenated codes can be achieved; indeed the performance is almost as close to the Shannon limit as that of Turbo codes. A linear code may be described in terms of a generator matrix G or in terms of a parity check matrix H, which satisfies Hx = 0 for all codewords x. In 1962, Gallager reported work on binary codes defined in terms of low density parity check matrices (abbreviated ‘GL codes’) [5, 6]. The matrix H was defined in a non-systematic form; each column of H had a small weight (e.g., 3) and the weight per row was also uniform; the matrix H was constructed at random subject to these constraints. Gallager proved distance properties of these codes and described a probability-based decoding algorithm with promising empirical performance. However it appears that GL codes have been generally forgotten, the assumption perhaps being that concatenated codes [4] were superior for practical purposes (R.G. Gallager, personal communication). During our work on MN codes [8] we realised that it is possible to create ‘good’ codes from very sparse random matrices, and to decode them (even beyond their minimum distance) using approximate probabilistic algorithms. We eventually reinvented Gallager’s decoding algorithm and GL codes. In this paper we report the empirical performance of these codes on Gaussian channels. We have proved theoretical properties of GL codes (essentially, that the channel coding theorem holds for them) elsewhere [9]. GL codes can also be defined over GF (q). We are currently implementing this generalization. We created sparse random parity check matrices in the following ways. Construction 1A. An M by N matrix (M rows, N columns) is created at random with weight per column t (e.g., t = 3), and weight per row as uniform as possible, and overlap between any two columns no greater than 1. (The weight of a column is the number of non-zero elements; the overlap between two columns is their inner product.)
Size slicing: a hybrid approach to size inference in futhark

We present a shape inference analysis for a purely-functional language, named Futhark, that supports nested parallelism via array combinators such as map, reduce, filter}, and scan}. Our approach is to infer code for computing precise shape information at run-time, which in the most common cases can be effectively optimized by standard compiler optimizations. Instead of restricting the language or sacrificing ease of use, the language allows the occasional shape-dynamic, and even shape-misbehaving, constructs. Inherently shape-dynamic code is treated with a fall-back technique that preserves, asymptotically, the number of operations of the program and that computes and returns the array's shape alongside with its value. This approach leads to a shape-dependent system with existentially-quantified types, where static shape inference corresponds to eliminating existential quantifications from the types of program expressions. We optimize the common case to negligible overhead via size slicing: a technique that separates the computation of the array's shape from its values. This allows the shape to be calculated in advance and to be used to instantiate the previously existentially-quantified shapes of the value slice. We report negligible overhead, on several mini-benchmarks and three real-world applications.
Caveolar Localization Dictates Physiologic Signaling of β2-Adrenoceptors in Neonatal Cardiac Myocytes*

There is a growing body of evidence that G protein-coupled receptors function in the context of plasma membrane signaling compartments. These compartments may facilitate interaction between receptors and specific downstream signaling components while restricting access to other signaling molecules. We recently reported that β1- and β2-adrenergic receptors (AR) regulate the intrinsic contraction rate in neonatal mouse myocytes through distinct signaling pathways. By studying neonatal myocytes isolated from β1AR and β2AR knockout mice, we found that stimulation of the β1AR leads to a protein kinase A-dependent increase in the contraction rate. In contrast, stimulation of the β2AR has a biphasic effect on the contraction rate. The biphasic effect includes an initial protein kinase A-independent increase in the contraction rate followed by a sustained decrease in the contraction rate that can be blocked by pertussis toxin. Here we present evidence that caveolar localization is required for physiologic signaling by the β2AR but not the β1AR in neonatal cardiac myocytes. Evidence for β2AR localization to caveolae includes co-localization by confocal imaging, co-immunoprecipitation of the β2AR and caveolin 3, and co-migration of the β2AR with a caveolin-3-enriched membrane fraction. The β2AR-stimulated increase in the myocyte contraction rate is increased by ∼2-fold and markedly prolonged by filipin, an agent that disrupts lipid rafts such as caveolae and significantly reduces co-immunoprecipitation of β2AR and caveolin 3 and co-migration of β2AR and caveolin-3 enriched membranes. In contrast, filipin has no effect on β1AR signaling. These observations suggest that β2ARs are normally restricted to caveolae in myocyte membranes and that this localization is essential for physiologic signaling of this receptor subtype.
Akt3 is responsible for the survival and proliferation of embryonic stem cells

ABSTRACT The phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB/Akt) pathway plays an important role in regulating cell proliferation, metabolism, and survival. However, the distinct roles of Akt isoforms (Akt1, Akt2, and Akt3) in pluripotent stem cell maintenance are not fully defined. Using mouse embryonic stem cells (ESCs), we show that direct inhibition of Akt activity leads to ESC apoptosis. The Akt3, but not Akt1 or Akt2, activity specifically regulates this effect. Inhibiting Akt3 also leads to a cell cycle arrest at G1 phase. These regulatory roles of Akt3 are dependent on its kinase activity. Blocking the expression of Akt1 plus Akt2 in ESCs does not affect cell survival or proliferation, although blocking Akt1 aggravates the apoptotic effect induced by depletion of Akt3. We further show that blocking Akt3 in ESCs results in significant nuclear accumulation of p53, as well as the activation of its downstream targets, such as Mdm2, p21, and Fas. Inhibiting p53 and its downstream targets partially rescued the effects caused by Akt3-depletion. Our results revealed an Akt3 isoform-specific mechanism for ESC survival and proliferation involving the control of p53 activity. Summary: We identified that Akt isoform 3, but not Akt1 or Akt2, specifically regulates embryonic stem cell survival and proliferation. Mechanistically, this is achieved partially through controlling the p53 pathway activity.
Patch-clamp fluorometry–based channel counting to determine HCN channel conductance

The number of channels on a patch of membrane is a fundamental quantity for biophysical studies of ion channel mechanisms. Liu et al. develop a new method of channel counting based on patch-clamp fluorometry and use it to measure the single-channel conductance and ionic selectivity of HCN1 and HCN2 channels.
Dynamic properties of retino-geniculate synapses in the cat

Simultaneous recordings from relay cells in the lateral geniculate nucleus (LGN) and their retinal afferents were used to examine the rules governing the transmission of spikes across the retino-geniculate synapse. Retinal spikes that terminate short retinal interspike intervals are much more likely to be transmitted across the synapse than spikes terminating longer intervals. This facilitation can be observed for interspike intervals as long as 50 ms when retinal firing rates are low, but the range of effective intervals decreases exponentially as retinal firing rate increases. Contribution, the fraction of LGN spikes triggered by an individual retinal afferent, is typically much higher during visual stimulation than during maintained activity, and these differences are unrelated to presynaptic or postsynaptic firing rate. It is suggested that this effect is a manifestation of increased synchronization of spikes among retinal afferents to the geniculate cell during structured visual stimulation, and that this synchronization offers a means of enhancing signal-to-noise ratio at the retino-geniculate synapse. Cross-correlograms between geniculate burst spikes and retinal afferents often contain two distinct peaks; a short latency peak that results from direct coupling between burst spikes and retinal input spikes, and a longer latency peak that represents indirect coupling in which retinal spikes trigger the calcium spike underlying the burst. Direct coupling is most likely to occur for the later spikes in the burst, and is present regardless of whether the calcium spike underlying the burst is triggered by the same or a different retinal afferent. These results further illuminate the relationship between tonic and burst modes of retino-geniculate transmission and indicate that bursts in LGN relay cells can be viewed as a mechanism of signal amplification, producing signals whose timing is potentially related to the temporal structure of a stimulus, independent of presynaptic and postsynaptic firing rate. This mechanism also appears to capitalize on the synchronization that is present among parallel retinal afferents to a geniculate cell.
Maximum A Posteriori Bayesian Estimation of Mycophenolic Acid Pharmacokinetics in Renal Transplant Recipients at Different Postgrafting Periods

The aim of this study was to develop maximum a posteriori probability (MAP) Bayesian estimators of mycophenolic acid (MPA) pharmacokinetics (PK) capable of accurately estimating the MPA interdose AUC in renal transplant patients using a limited number of blood samples. The individual MPA plasma concentration-time profiles of 44 adult kidney transplant recipients were retrospectively studied: in 24 de novo transplant patients, 2 profiles were obtained on day 7 and day 30 after transplantation, and in 20 stable transplant patients, 1 profile was obtained in the stable period (>3 months). MPA was assayed by liquid chromatography-mass spectrometry. Concentration data were fitted using previously designed PK models, including 1 or 2Γ-distribution to describe the absorption rate. MAP-Bayesian estimations were performed using an in-house program. For each posttransplantation period, the limited sampling strategies (LSS) providing either the best determination coefficient or the lowest bias for AUC estimates with respect to trapezoidal AUCs were selected and compared with respect to the percentage of “clinically acceptable” AUC estimates (ie, within −20% to +20% of the true value) they yielded. A common LSS (blood samples collected at T20min, T1h, and T3h postdosing), convenient for all 3 periods, was also selected and validated: bias (RMSE%) values were −5.7% (20.5%), −8.2% (14.4%), and +0.4% (12.0%) on D7, D30, and for >M3 with respect to the reference values obtained using the trapezoidal rule, respectively. For the first time, MAP-Bayesian estimators of MPA systemic exposure at different posttransplantation periods (early as well as later periods) could be designed. They have since been used for MPA dose adaptation in concentration-controlled studies as well as for MPA therapeutic drug monitoring in clinical practice.
Manifest disease, risk factors for sudden cardiac death, and cardiac events in a large nationwide cohort of predictively tested hypertrophic cardiomyopathy mutation carriers: determining the best cardiological screening strategy.

AIMS We investigated the presence of a clinical diagnosis of hypertrophic cardiomyopathy (HCM), risk factors for sudden cardiac death (SCD), and cardiac events during follow-up in predictively tested-not known to have a clinical diagnosis of HCM before the DNA test-carriers of a sarcomeric gene mutation and associations with age and gender to determine the best cardiological screening strategy. METHODS AND RESULTS One hundred and thirty-six (30%) of 446 mutation carriers were diagnosed with HCM at one or more cardiological evaluation(s). Male gender and higher age were associated with manifest disease. Incidence of newly diagnosed manifest HCM was <10% per person-year under the age of 40 years and >10% in older carriers, although numbers were small in carriers <15 years. Twenty-three percent of carriers, with and without manifest disease, had established risk factor(s) for SCD (no significant difference). During an average follow-up of 3.5 ± 1.7 years two carriers, both with manifest disease, died suddenly (0.13% per person-year). A high-risk status for SCD (≥2 risk factors and manifest HCM) was present in 17 carriers during follow-up (2.4% per person-year). Age but not gender was associated with a high-risk status for SCD. CONCLUSION Thirty percent of carriers had or developed manifest HCM after predictive DNA testing and risk factors for SCD were frequently present. Our data suggest that the SCD risk is low and risk stratification for SCD can be omitted in carriers without manifest disease and that frequency of cardiological evaluations can possibly be decreased in carriers between 15 and 40 years as long as hypertrophy is absent.
S1 Ribosomal Protein Functions in Translation Initiation and Ribonuclease RegB Activation Are Mediated by Similar RNA-Protein Interactions

The ribosomal protein S1, in Escherichia coli, is necessary for the recognition by the ribosome of the translation initiation codon of most messenger RNAs. It also participates in other functions. In particular, it stimulates the T4 endoribonuclease RegB, which inactivates some of the phage mRNAs, when their translation is no longer required, by cleaving them in the middle of their Shine-Dalgarno sequence. In each function, S1 seems to target very different RNAs, which led to the hypothesis that it possesses different RNA-binding sites. We previously demonstrated that the ability of S1 to activate RegB is carried by a fragment of the protein formed of three consecutive domains (domains D3, D4, and D5). The same fragment plays a central role in all other functions. We analyzed its structural organization and its interactions with three RNAs: two RegB substrates and a translation initiation region. We show that these three RNAs bind the same area of the protein through a set of systematic (common to the three RNAs) and specific (RNA-dependent) interactions. We also show that, in the absence of RNA, the D4 and D5 domains are associated, whereas the D3 and D4 domains are in equilibrium between open (noninteracting) and closed (weakly interacting) forms and that RNA binding induces a structural reorganization of the fragment. All of these results suggest that the ability of S1 to recognize different RNAs results from a high adaptability of both its structure and its binding surface.
A Model for Hedging Load and Price Risk in the Texas Electricity Market

Energy companies with commitments to meet customers' daily electricity demands face the problem of hedging load and price risk. We propose a joint model for load and price dynamics, which is motivated by the goal of facilitating optimal hedging decisions, while also intuitively capturing the key features of the electricity market. Driven by three stochastic factors including the load process, our power price model allows for the calculation of closed-form pricing formulas for forwards and some options, products often used for hedging purposes. Making use of these results, we illustrate in a simple example the hedging benefit of these instruments, while also evaluating the performance of the model when fitted to the Texas electricity market.
Unsupervised face recognition from image sequences based on clustering with attraction and repulsion

We propose a new method for unsupervised face recognition from time-varying sequences of face images obtained in real-world environments. Two types of forces, attraction and repulsion, operate across the spatio-temporal facial manifolds, to autonomously organize the data without relying on any category-specific information provided in advance. Experiments with real-world data gathered over a period of several months and including both frontal and side-view faces were used to evaluate the method and encouraging results were obtained The proposed method can be used in video surveillance systems or for content-based information retrieval.
Design of selective production of sophorolipids by Rhodotorula bogoriensis through nutritional requirements

Rhodotorula bogoriensis is known as the producer of longer chain acidic sophorolipids (SLs) with a unique hydroxylation position where the sophorose unit is linked to the 13‐hydroxydocosanoic acid. The influence of initial inoculum concentration, hydrophilic and hydrophobic carbon, and nitrogen sources on R. bogoriensis growth and SL production was evaluated to obtain a selective SL production. Experiments took place in microtiter plates, used as minireactors, after the verification of its suitability compared with shake flasks.
The relaxation method for a special class of linear programming problems

An iterative method for solving a class of linear programming problems whose constraints satisfy certain diagonal dominance condition is proposed. This method partitions the original linear program into subprograms where each subprogram corresponds uniquely to a variable of the problem. At each iteration, one of the sub-programs is solved by adjusting its corresponding variable, while the other variables are held constant. This philosophy of successively changing one variable at a time is reminiscent of the coordinate relaxation method. The algorithmic mapping underlying this method is shown to be monotone and contractive. Then, using the contractive property, the method is shown to converge even when implemented in an asynchronous, distributed manner, and that its rate of convergence can be determined from the synchronization parameter. An illustration example is given.
The Günther Tulip retrievable filter: prolonged temporary filtration by repositioning within the inferior vena cava.

PURPOSE To report experience with the retrievable Günther Tulip filter (GTF) as a means of temporary caval filtration for the prevention of pulmonary embolism (PE) with use of a technique that prolongs filter dwell time beyond 14 days. MATERIALS AND METHODS Eighty-eight GTFs were implanted in 87 patients. The GTFs were placed with the intention of retrieval in all patients within 14 days after initial implantation. In 23 of the 87 patients (26%), there was a need to prolong temporary caval filtration beyond the recommended period of 14 days. This was successfully achieved with use of percutaneous techniques from the right internal jugular vein whereby the filter was repositioned to a different location within the inferior vena cava (IVC) before definitive device removal. RESULTS Of 88 GTFs implanted in 87 patients, 70 were successfully retrieved and 18 were left in place permanently. Forty-seven filters in 46 patients were removed after initial implantation with no need for percutaneous repositioning within the IVC to prolong dwell time (mean dwell time, 13 days). In the 23 patients who required repositioning of 23 GTFs within the IVC to prolong temporary caval filtration, the mean dwell time was 34.8 days; the mean number of repositioning procedures was 1.5, the mean time between repositioning procedures was 13.8 days, and the mean fluoroscopy time was 4.4 minutes in patients in whom filter retrieval was attempted. One patient underwent placement and subsequent removal of the GTF twice for perioperative prophylaxis against PE on two separate occasions. No filters were misplaced in an unintended location or tilted (>15 degrees ) in relation to the main caval axis after deployment. In one patient, a GTF became permanently fixed in the IVC 16 days after initial implantation and could not be removed percutaneously. Nine patients had mild or moderate-sized cervical hematomas. One patient had recurrent asymptomatic PE 2 months after filter insertion. CONCLUSION Dwell times of 14 days can be achieved in most patients before device removal. Prolongation of the dwell time beyond 14 days can be safely and easily achieved by performing percutaneous repositioning of the device within the IVC via a jugular approach.
CMP and self-shadowing effect of overlay mark in metal sputtering process

Overlay mismatch of pre/post etch on metal layer is caused by asymmetric metal deposition on overlay mark. The major components of the mismatch are known to be composed of wafer scale and rotation caused by self-shadowing effect and CMP process, respectively. The behavior of each component was observed according to the changes in overlay mark shapes, metal thickness and CMP process conditions in this study. The overlay difference according to metal overhang on overlay mark was also investigated. It was found that overlay mismatch was reduced when the metal overhang on overlay mark happens, and over-polishing overlay mark during W CMP prevents formation of the metal overhang and increases wafer scale mismatch.
Rate-distortion based video coding with adaptive mean-removed vector quantization

In this paper we improve the rate-distortion performance of a previously proposed video coder based on frame replenishment and adaptive mean-removed vector quantization. This is realized by determining for each block of a given frame the optimal encoding mode in the rate-distortion sense. The algorithm is a new contribution to very low bit rate video coding with adaptive vector quantization suitable for videophone applications. Experimental results comparing the two coders for several test sequences at different bit rates are provided.