Miracle-dz/UniFAR-FTUs huggingface dataset:
A-Kinase Anchor Proteins as Potential Regulators of Protein Kinase A Function in Oocytes1

Abstract In the mammalian oocyte, the cAMP-dependent protein kinase (PKA) has critical functions in the maintenance of meiotic arrest and oocyte maturation. Because PKA is spatially regulated, its localization was examined in developing oocytes. Both regulatory subunits (RI and RII) and the catalytic subunit (C) of PKA were found in oocytes and metaphase II-arrested eggs. In the oocyte, RI and C were predominantly localized in the cortical region, while RII showed a punctate distribution within the cytoplasm. After maturation to metaphase II, RI remained in the cortex and was also localized to the meiotic spindle, while RII was found adjacent to the spindle. C was diffuse within the cytoplasm of the egg but was enriched in the cytoplasm surrounding the metaphase spindle, much like RII. The polarized localization and redistribution of RI, RII, and C suggested that PKA might be tethered by A-kinase anchor proteins (AKAPs), proteins that tether PKA close to its physiological substrates. An AKAP, AKAP140, was identified that was developmentally regulated and phosphorylated in oocytes and eggs. AKAP140 was shown to be a dual-specific AKAP, having the ability to bind both RI and RII. By compartmentalizing PKA, AKAP140 and/or other AKAPs could spatially regulate PKA activity during oocyte development.
Modern Statistical Modeling Approaches for Analyzing Repeated-Measures Data

Background:Researchers often describe the collection of repeated measurements on each individual in a study design. Advanced statistical methods, namely, mixed and marginal models, are the preferred analytic choices for analyzing this type of data. Objective:The aim was to provide a conceptual understanding of these modeling techniques. Approach:An understanding of mixed models and marginal models is provided via a thorough exploration of the methods that have been used historically in the biomedical literature to summarize and make inferences about this type of data. The limitations are discussed, as is work done on expanding the classic linear regression model to account for repeated measurements taken on an individual, leading to the broader mixed-model framework. Results:A description is provided of a variety of common types of study designs and data structures that can be analyzed using a mixed model and a marginal model. Discussion:This work provides an overview of advanced statistical modeling techniques used for analyzing the many types of correlated . data collected in a research study.
Characterization of a gene encoding tRNA nucleotidyltransferase from Candida glabrata

A gene encoding ATP (CTP):tRNA nucleotidyltransferase (EC2.7.7.25) was isolated from Candida (Torulopsis) glabrata by complementation in Saccharomyces cerevisiae. The predicted amino acid sequence of the protein revealed a large region with high sequence similarity to members of the Class II group of the nucleotidyltransferase superfamily and an N‐terminal region characteristic of a mitochondrial targeting sequence. The essential role of the carboxylates within the conserved DXD and RRD motifs was confirmed by mutagenesis. C. glabrata strains bearing truncated CCA1 genes that lacked sequences encoding the putative mitochondrial targeting peptide were unable to grow on non‐fermentable carbon sources but were able to grow on a fermentable carbon source. These results suggest that, as in S. cerevisiae, the C. glabrata CCA‐adding enzyme is a sorting isozyme that functions in multiple cellular compartments. Mapping of the 5′‐ends of primary transcripts of CCA1 revealed multiple transcription start sites located both upstream of and between two in‐frame start codons. When the cells were cultured on a non‐fermentable carbon source the longer transcripts appeared more abundant, suggesting that the choice of transcription start sites was influenced by carbon source. The shorter transcripts, which lacked sequences encoding the mitochondrial targeting information, were more predominant in cells grown on glucose. These observations suggest that expression of CCA‐adding isozymes in C. glabrata may be regulated. The DNA sequence has been assigned GenBank Accession No. AF098803. Copyright © 2002 John Wiley & Sons, Ltd.
Amidophosphoribosyltransferase Limits the Rate of Cell Growth-linked de Novo Purine Biosynthesis in the Presence of Constant Capacity of Salvage Purine Biosynthesis*

Factors controlling relative flux rates of thede novo and salvage pathways of purine nucleotide biosynthesis during animal cell growth are not fully understood. To examine the relative role of each pathway for cell growth, three cell lines including CHO K1 (a wild-type Chinese hamster ovary fibroblast cell line), CHO ade −A (an auxotrophic cell line deficient of amidophosphoribosyltransferase (ATase), a presumed rate-limiting enzyme of the de novo pathway), and CHO ade −A transfected with human ATase cDNA (−A+hATase) resulting in 30–350% of the ATase activity of CHO K1, were cultured in purine-rich or purine-free media. Based on the enzyme activities of ATase and hypoxanthine phosphoribosyltransferase, the metabolic rate of the de novo and salvage pathways, the rate of cell growth (growth rate) in three cell lines under various culture conditions, and the effect of hypoxanthine infusion on the metabolic rate of thede novo pathway in rat liver, we concluded the following. 1) In −A+hATase transfectants, ATase activity limits the rate of the de novo pathway, which is closely linked with the growth rate. 2) Purine nucleotides are synthesized preferentially by the salvage pathway as long as hypoxanthine, the most essential source of purine salvage, can be utilized, which was confirmed in rat liver in vivo by hypoxanthine infusion. The preferential usage of the salvage pathway results in sparing the energy expenditure required for de novo synthesis. 3) The regulatory capacity of the de novo pathway (about 200%) was larger than that of the salvage pathway (about 20%) with constant hypoxanthine phosphoribosyltransferase activity.
Treating Scars: Addressing Surface, Volume, and Movement to Expedite Optimal Results. Part 2: More‐Severe Grades of Scarring

Background The management of scarring (after acne, surgery, or disease) is an ongoing challenge. Methods This is the second of two reviews and will use a grading scale of disease burden to classify scarred patients. Treatment discussion will concentrate on procedures exerting effect on volume and surface changes and the effects of movement. Results Treatment relevant to the type and severity of scarring will be discussed and tabulated treatment plans outlined. Conclusion Severe grades of scarring often require a combination of filling agents for volume deficit, injectable agents for hypertrophic disease, neurotoxins to effect movement, and fractionated and ablative resurfacing for surface changes.
Psychopathology among Cocaine Abusers Entering Treatment

A number of different indicators of psychopathology were assessed in this study of 76 cocaine and crack abusers who entered outpatient treatment in New York City between June and December 1987. The majority (75%) had used cocaine for 4 years or more, and the majority (62%) spent over one thousand dollars a month on cocaine in the 6 months before entry into treatment. Forty-seven percent of the sample were found to be clinically depressed. Phobic disorders were the only other axis I diagnoses found in addition to depression, and all persons who were found to have phobic disorders also were diagnosed as having some form of depressive disorder. The four most common axis II diagnoses were antisocial personality (21%), passive-aggressive (21%), borderline (18%) and self-defeating (18%). Subjects were classified as falling into one of the following three categories of a newly developed “psychopathology classification”: a) no diagnosed psychopathology except substance abuse or dependency; b) one or more axis II diagnoses, but no axis I diagnoses except for substance abuse or dependency; c) at least one axis I diagnosis in addition to drug disorders whether or not accompanied by an axis II diagnosis. Mean scores on subscales and total score on the SCL-90, as well as total score on the Beck Depression Inventory, were ordered by category of the classification scheme, with those having no diagnosed psychopathology except substance abuse having the lowest score and persons in the third category having the highest score. Persons diagnosed as having depressive disorders were found to have started to use tobacco, marijuana, and cocaine at a significantly earlier age than persons not suffering from these disorders. Although not conclusive, these data suggest that such persons are especially likely to have severe involvement with drugs.
Clinical Progression and Cytokine Profiles of Middle East Respiratory Syndrome Coronavirus Infection

Clinical progression over time and cytokine profiles have not been well defined in patients with Middle East respiratory syndrome coronavirus (MERS-CoV) infection. We included 17 patients with laboratory-confirmed MERS-CoV during the 2015 outbreak in Korea. Clinical and laboratory parameters were collected prospectively. Serum cytokine and chemokine levels in serial serum samples were measured using enzyme-linked immunosorbent assay. All patients presented with fever. The median time to defervescence was 18 days. Nine patients required oxygen supplementation and classified into severe group. In the severe group, chest infiltrates suddenly began to worsen around day 7 of illness, and dyspnea developed at the end of the first week and became apparent in the second week. Median time from symptom onset to oxygen supplementation was 8 days. The severe group had higher neutrophil counts during week 1 than the mild group (4,500 vs. 2,200/µL, P = 0.026). In the second week of illness, the severe group had higher serum levels of IL-6 (54 vs. 4 pg/mL, P = 0.006) and CXCL-10 (2,642 vs. 382 pg/mL, P < 0.001). IFN-α response was not observed in mild cases. Our data shows that clinical condition may suddenly deteriorate around 7 days of illness and the serum levels of IL-6 and CXCL-10 was significantly elevated in MERS-CoV patients who developed severe diseases.
Organ culture stability of the intervertebral disc: Rat versus rabbit

There is a need to develop mechanically active culture systems to better understand the role of mechanical stresses in intervertebral disc (IVD) degeneration. Motion segment cultures that preserve the native IVD structure and adjacent vertebral bodies are preferred as model systems, but rapid ex vivo tissue degeneration limits their usefulness. The stability of rat and rabbit IVDs is of particular interest, as their small size makes them otherwise suitable for motion segment culture. The goal of this study was to determine if there are substantial differences in the susceptibility of rat and rabbit IVDs to culture‐induced degeneration. Lumbar IVD motion segments were harvested from young adult male Sprague–Dawley rats and New Zealand White rabbits and cultured under standard conditions for 14 days. Biochemical assays and safranin‐O histology showed that while glycosaminoglycan (GAG) loss was minimal in rabbit IVDs, it was progressive and severe in rat IVDs. In the rat IVD, GAG loss was concomitant with the loss of notochordal cells and the migration of endplate (EP) cells into the nucleus pulposus (NP). None of these changes were evident in the rabbit IVDs. Compared to rabbit IVDs, rat IVDs also showed increased matrix metalloproteinase‐3 (MMP‐3) and sharply decreased collagen type I and II collagen expression. Together these data indicated that the rabbit IVD was dramatically more stable than the rat IVD, which showed culture‐related degenerative changes. Based on these findings we conclude that the rabbit motion segments are a superior model for mechanobiologic studies. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31: 838–846, 2013
Performance of QSTBC and VBLAST Algorithms for MIMO Channels in Tunnels

The performance of multiple-input-multiple-output (MIMO) systems is strongly affected by the properties of the channel matrices. In tunnels, despite the small angular spreads of the rays, it has already been shown that the average mutual information can be strongly enhanced using MIMO rather than single-input-single-output (SISO). However, limited information is available on the improvement of the bit error rate (BER), assuming a fixed throughput and transmitted power. In this letter, starting from measured transfer matrices in a straight arched tunnel, MIMO performances based on VBLAST or QSTBC algorithms are compared to those of a SISO link. Furthermore, the use of polarization diversity is also studied.
Effects of Probiotic Supplementation on Pancreatic β-cell Function and C-reactive Protein in Women with Polycystic Ovary Syndrome: A Randomized Double-blind Placebo-controlled Clinical Trial

Background: Polycystic ovary syndrome (PCOS) is a polygenic endocrine disorder in women of reproductive age that lead to infertility. The aim of this study was to investigate the effects of probiotic on pancreatic β-cell function and C-reactive protein (CRP) in PCOS patients. Methods: This randomized double-blind placebo-controlled clinical trial was conducted among 72 women aged 15–40 years old diagnosed with PCOS. Participants were randomly assigned to two groups receiving: (1) Probiotic supplements (n = 36), (2) placebo (n = 36) for 8-week. Fasting blood samples were taken at baseline and after 8-week of intervention. Results: Probiotic supplementation, compare with placebo, reduced fasting blood sugar (−4.15 ± 2.87 vs. 2.57 ± 5.66 mg/dL, respectively P = 0.7), serum insulin levels in crude model (−0.49 ± 0.67 vs. 0.34 ± 0.82 μIU/mL, respectively, P = 0.09), homeostasis model of assessment-insulin resistance score (−0.25 ± 0.18 vs. −0.05 ± 0.18, respectively, P = 0.14) nonsignificantly. Serum insulin levels after adjustment with covariates reduced significantly in probiotic group (P = 0.02). We did not found any significant differences in mean changes of CRP between groups (−0.25 ± 0.18 vs. −0.05 ± 0.18, respectively, P = 0.14). Conclusions: A 8-week multispecies probiotics supplementation had nonsignificantly beneficial effect on pancreatic β-cell function and CRP in PCOS patients. After adjustment for some covariates, serum insulin changes were significantly different between groups.
How Much Training is Required for Multiuser Mimo?

An M-element antenna array (the base station) transmits, on the downlink, K les M sequences of QAM symbols selectively and simultaneously to K autonomous single-antenna terminals through a linear pre-coder that is the pseudo-inverse of an estimate of the forward channel matrix. We assume time-division duplex (TDD) operation, so the base station derives its channel estimate from taurp pilot symbols which the terminals transmit on the reverse link. A coherence interval of T symbols is expended as follows: taurp reverse pilot symbols, one symbol for computations, and (T-l-taurp) forward QAM symbols for each terminal For a given coherence interval, number of base station antennas, and forward- and reverse-SINR's we determine the optimum number of terminals to serve simultaneously and the optimum number of reverse pilot symbols to employ by choosing these parameters to maximize a lower bound on the net sum-throughput. The lower bound rigorously accounts for channel estimation error, and is valid for all SINR's. Surprisingly it is always advantageous to increase the number of base station antennas, even when the reverse SINR is low and the channel estimate poor: greater numbers of antennas enable us to climb out of the noise and to serve more terminals. Even within short coherence intervals (T= 10 symbols) and with low SINR's (-10.0 dB reverse, 0.0 dB forward) given large numbers of base station antennas (M ges 16 ) it is both feasible and advantageous to learn the channel and to serve a multiplicity of terminals simultaneously as well.
Scaling Service-Oriented Applications into Geo-distributed Clouds

With the significant prevalence of cloud computing, more and more data centers are built to host and deliver various online services. However, a key challenge faced by service providers is how to scale their applications into geo-distributed data centers to improve application performance as well as minimizing the operational cost. While most existing deployment methods ignore the service dependencies in an application, this paper proposes a general dynamic service deployment framework to bridge this gap, in which a deployment manager and a local scheduler are designed to optimize data center selection and auto-scale the service instances in each data center respectively. More specifically, we formulate the deployment problem across multiple data centers as a compact minimization model, which can be solved efficiently by a genetic algorithm. To evaluate the performance of our approach, extensive experiments are conducted based on a large-scale real-world latency dataset. The experimental results show that our approach substantially outperforms the other existing methods.
Analysis of Agrobacterium tumefaciens plasmid pTiC58 replication region with a novel high-copy-number derivative

The origin of replication, ori, of the nopaline tumor-inducing plasmid, pTiC58, mapped in a region that shares sequence homology with octopine plasmids pTiAch5 and pTiB6. Within this region, the minimum amount of DNA necessary for maintaining autonomous replication was a 2.6-kilobase region, which also comprised the incompatibility function inc. pTiC58 derivatives containing inc were incompatible with Agrobacterium tumefaciens plasmids pTiC58, pTiD1439, pTiAch5, pTi15955, and pTiA5 and were compatible with A. rhizogenes plasmid pRi12. Situated adjacent to the origin region was a 1.5-kilobase par segment involved in stable inheritance of pTiC58 under nonselective growth conditions. When par was present, plasmid maintenance approached that of the wild-type pTiC58. Rapid loss from the cell population was observed for plasmids not containing this locus. Another 1.5-kilobase region, cop, positively regulated pTiC58 copy number, enabling certain pTiC58 derivatives to exist at a copy number up to 80 times higher than that of wild-type pTiC58. Deletions within the cop locus resulted in reduced copy number. The ori/inc regions were flanked on either side by the par and cop loci.
A comprehensive approach for accurate measurement of proton-proton coupling constants in the sugar ring of DNA.

Stereo-selectivedeuteration has been explored as an approach for improving the accuracy of NMR-derived, three-bond vicinal proton-proton coupling constants in the 12-base-pair DNA Dickerson sequence [d(CGCGAATTCGCG)(2)]. The coupling constants are useful for DNA structure determination in restrained molecular dynamics calculations. Specifically, the A5 and A6 residues were prepared with the H2" proton stereo-selectively replaced with a deuteron. Deuteration of the H2" leads to a 42-fold reduction in the transverse cross-relaxation rate of the H2' spin, effectively negating the contribution of transverse cross relaxation to the cross peak frequencies and phases. Calculated linewidth and polarization transfer functions indicated that the reduced dipolar interaction is also expected to result in a significant increase in intensity for all cross peaks involving the H1', H2', or H3' spin. The spectral complexity is also reduced by selective deuteration. Time-shared homonuclear decoupling of passive spins during acquisition was implemented, reducing the spin system, in some cases, to an effectively isolated two-spin system. This enables the use of a 90 degrees mixing pulse instead of the 35 degrees pulse commonly used in standard P.E. COSY experiments, leading to an additional 75% increase in signal intensity. Selective excitation pulses were used to reduce the number of increments required in the indirect dimension by as much as a factor of 4. The cumulative improvement in sensitivity is striking, approaching three orders of magnitude per unit time. Separate experiments, referred to as Stripe-COSY and Superstripe-COSY, were optimized for each coupling constant measured. Finally, J-doubling was used to obtain the most accurate peak separations. This comprehensive approach shows promise as an effective method for extracting highly accurate homonuclear vicinal coupling constants in DNA.
Cost Analysis of Community-Based Daily and Weekly Programs for Treatment of Moderate and Mild Wasting among Children on Nias Island, Indonesia

Background Ready-to-use food in the form of biscuits (RUF-Nias biscuit) was locally produced for rehabilitation of moderately and mildly wasted (weight-for-height z-score ≥ −3 to < −1.5 SD) children on Nias Island, Indonesia. Daily programs were performed in semiurban settings, and weekly programs took place in rural areas. Objective To analyze the cost of daily and weekly distribution and supervision of RUF-Nias biscuit programs. Methods The costs of the daily and weekly programs were derived from the financial report and interviews with program implementers and participating households. Costs were calculated on the basis of total rehabilitation costs per child per day required to achieve a target weight-for-height z-score ≥ −1.5 SD in daily and weekly programs. Results Institutional costs to the implementing organization were similar for both programs (approximately US$4 per child per day). The daily programs resulted in a significantly higher proportion of recovered children (78.6% vs. 65.4%) and higher weight gain (3.7 vs. 2.2 g/kg/day) than the weekly programs. About 6% to 7% of the total cost of the programs was accounted for by locally produced RUF-Nias biscuits. The social cost borne by the community for the weekly programs was about half that for the daily programs. Conclusions The daily programs achieved better results for the implementing organization than the weekly programs; however, the weekly programs were preferred by the community because of the lower time constraints and the lower opportunity cost of time. The willingness of community and household members to invest their time in more intensive activities in the daily programs led to better program outcomes.
The role of Epstein–Barr virus‐encoded small RNAs (EBERs) in oncogenesis

Epstein–Barr virus (EBV)‐encoded RNAs (EBERs) are the most abundant viral transcripts in latently EBV‐infected cells. Recently, we found that EBERs play a key role in the maintenance of malignant phenotypes of Burkitt's lymphoma (BL) cells. They confer clonability in soft agarose, tumorigenicity in immunodeficient mice, resistance to apoptosis and induction of interleukin (IL)‐10, which acts as an autocrine growth factor of BL cells. Furthermore, we demonstrated that EBERs confer resistance to interferon (IFN)‐α‐induced apoptosis by inhibition of double‐stranded (ds) RNA‐activated protein kinase (PKR), which is the key mediator of the antiviral effect of IFN‐α. These studies provide a new notion that RNA molecules contribute to oncogenesis. Copyright © 2002 John Wiley & Sons, Ltd.