Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolism-related enzyme alterations identified by proteomic analysis in human renal cell carcinoma

The renal cell carcinoma (RCC) is one of the most common types of kidney neoplasia in Western countries; it is relatively resistant to conventional chemotherapy and radiotherapy. Metabolic disorders have a profound effect on the degree of malignancy and treatment resistance of the tumor. However, the molecular characteristics related to impaired metabolism leading to the initiation of RCC are still not very clear. In this study, two-dimensional electrophoresis (2-DE) and mass spectra (MS) technologies were utilized to identify the proteins involved in energy metabolism of RCC. A total of 73 proteins that were differentially expressed in conventional RCC, in comparison with the corresponding normal kidney tissues, were identified. Bioinformatics analysis has shown that these proteins are involved in glycolysis, urea cycle, and the metabolic pathways of pyruvate, propanoate, and arginine/proline. In addition, some were also involved in the signaling network of p53 and FAS. These results provide some clues for new therapeutic targets and treatment strategies of RCC.
Application of an inexpensive and high‐throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs

We describe the application of a simple, low‐cost, and effective method of DNA extraction (hot sodium hydroxide and Tris, HotSHOT) to the diapausing propagules of continental aquatic invertebrates for its use in PCR amplification. We illustrate the use of the technique in cladocerans, rotifers, anostracans, notostracans, and copepod diapausing eggs. We compare the performance of the HotSHOT technique to the currently most widely used method for DNA extraction of zooplankton eggs and individuals, the chelating resin (or Chelex) technique. The HotSHOT technique overcomes several of the problems posed by Chelex and permits easy optimization for its use with 96‐well plates for high‐throughput DNA extraction and subsequent genetic characterization. We foresee a wide use of this technique in the future from DNA barcoding of diapausing stages to the genetic characterization of the diapausing egg banks of continental aquatic invertebrates.
Sparse online learning with bandit feedback

The bandit classification problem considers learning the labels of a time-indexed data stream under a mere " hit-or-miss " binary guiding. Adapting the OVA (" one-versus-all ") hinge loss setup, we develop a sparse and lightweight solution to this problem. The issued sequential norm-minimal update solves the classification problem in finite time in the separable case, provided enough redundancy is present in the data. An O(√ T) regret in moreover expected in the non-separable case. The algorithm shows effectiveness on both large scale text-mining and machine learning datasets, with (i) a favorable comparison with the more demanding confidence-based second-order bandits setups on large scale datasets and (ii) a good sparsity and efficacy when a kernel approach is applied to non-separable datasets.
Southern Hemisphere atmospheric circulation effects of the 1991 Mount Pinatubo eruption

Global average cooling and Northern Hemisphere winter warming are well‐known climatic responses to the June 15, 1991 eruption of the Mount Pinatubo volcano in the Philippines. Here we investigate the Southern Hemisphere response. Using National Centers for Environmental Prediction/National Center for Atmospheric Research Reanalysis, European Centre for Medium‐Range Weather Forecasting Reanalysis, and simulations with the National Aeronautics and Space Administration Goddard Institute for Space Studies ModelE climate model, we find that, in contrast to the Northern Hemisphere, there were no strong significant anomalies in atmospheric circulation in the Southern Hemisphere. We examined 50 mb and 500 mb circulation patterns, as well as the Southern Hemisphere Annular Mode index, and found no consistent significant anomalies associated with the volcanic eruption, or the previous large volcanic eruptions of the past 50 years, the 1963 Agung and 1982 El Chichón eruptions. The few anomalies that occurred after Pinatubo are consistent with patterns found during an El Niño event, which took place that same year.
Prolonged obstructive jaundice in infancy. V. The genetic components in neonatal hepatitis.

During the past few years increasing attention has been directed toward a group of infants with prolonged obstructive jaundice not associated with erythroblastosis fetalis or biliary atresia. This syndrome is characterized by onset of jaundice during the first weeks of life, acholic stools, dark urine, and moderate hepatomegaly and splenomegaly. Laboratory studies on these infants show their urine to contain bile and their stools to be free of both bile and urobilinogen, the flocculation tests of liver function being usually negative. The one-minute and total serum bilirubin are, however, always elevated and show either a slowly falling or variable trend. Histological examination of the liver reveals focal or widespread hepatocellular degeneration, often with the formation of multinucleated liver cells or liver "giant cells. " Follow-up studies have revealed that about 60% of these infants recover without sequelae, some develop cirrhosis despite treatment, and a small group die as a result of
Initiation of dieting among adolescent females.

OBJECTIVE This brief report identifies the factors that distinguish girls who have begun dieting recently from those who have never dieted, using Huon and Strong's (International Journal of Eating Disorders 23:361-369, 1998) model of dieting. METHOD Sixty-two initiating dieters were carefully matched with 62 never dieters, according to school, grade, age, language spoken at home, and country of birth. Both groups completed a battery of questionnaires that assessed their dieting status, perceived social influence to diet, conformity disposition, assertiveness, and familial context. RESULTS A discriminant function analysis showed that initiating dieters and never dieters could be distinguished most clearly by their levels of peer and parental influence. Initiating dieters conformed and complied more to their parents. They were also more competitive with their peers than were the girls who had never dieted. Perceived supportiveness of fathers was also found to set apart those girls who had never dieted. DISCUSSION Girls who are just beginning to diet differ from those who have never dieted, predominantly in terms of their perceived social influence. The forms of parental influence that distinguish the two groups differ in nature from the type of influence exerted by peers.
Differential regulation of Cdc2 and Aurora-A in Xenopus oocytes: a crucial role of phosphatase 2A

The success of cell division relies on the activation of its master regulator Cdc2-cyclin B, and many other kinases controlling cellular organization, such as Aurora-A. Most of these kinase activities are regulated by phosphorylation. Despite numerous studies showing that okadaic acid-sensitive phosphatases regulate both Cdc2 and Aurora-A activation, their identity has not yet been established in Xenopus oocytes and the importance of their regulation has not been evaluated. Using an oocyte cell-free system, we demonstrate that PP2A depletion is sufficient to lead to Cdc2 activation, whereas Aurora-A activation depends on Cdc2 activity. The activity level of PP1 does not affect Cdc2 kinase activation promoted by PP2A removal. PP1 inhibition is also not sufficient to lead to Aurora-A activation in the absence of active Cdc2. We therefore conclude that in Xenopus oocytes, PP2A is the key phosphatase that negatively regulates Cdc2 activation. Once this negative regulator is removed, endogenous kinases are able to turn on the activator Cdc2 system without any additional stimulation. In contrast, Aurora-A activation is indirectly controlled by Cdc2 activity independently of either PP2A or PP1. This strongly suggests that in Xenopus oocytes, Aurora-A activation is mainly controlled by the specific stimulation of kinases under the control of Cdc2 and not by downregulation of phosphatase.
Comparison of clonidine response in the treatment of attention-deficit hyperactivity disorder with and without comorbid tic disorders.

OBJECTIVE Clonidine has been suggested as an alternative pharmacotherapy for patients with attention-deficit hyperactivity disorder (ADHD) and comorbid tic disorders. To examine the efficacy of clonidine in this population of children, the use of clonidine in the treatment of children with ADHD with and without comorbid tic disorders was examined in a retrospective chart review of 54 children over a 4-year period. METHOD Treatment was administered openly to these patients in a Pediatric Psychopharmacology Clinic, and response was assessed using clinical global improvement measures. RESULTS Clonidine treatment resulted in improvement in both the ADHD (39/54; 72%) and tic symptoms (18/24; 75%) groups. The findings suggested that the children with ADHD with comorbid tic disorders (23/24; 96%) have a more frequent positive behavioral response to clonidine than children with ADHD without comorbid tic disorders (16/30; 53%). CONCLUSIONS This report provides further support of a role for clonidine in the treatment of children with ADHD, particularly for those with comorbid tic disorders.
Large Eddy Simulation of Pulsating Flow before and after CoA Repair: CFD for Intervention Planning

Large eddy simulation was applied to investigate hemodynamics in a model with coarctation of the aorta (CoA) and poststenotic dilatation. Special focus was put on the role of hemodynamics for success of CoA repair. Several parameters previously identified as related to cardiovascular disease were studied. Known risk factors were observed both with CoA and after repair, and the restoration of the anatomy seems to be crucial for a successful result.
Sperm parameters in men with suspected infertility. Sperm characteristics, strict criteria sperm morphology analysis and hypoosmotic swelling test.

OBJECTIVE To determine the distribution of sperm abnormalities in a population of suspected infertile men presenting for the initial investigation of male factor infertility. STUDY DESIGN Results obtained in the analysis of sperm viability, motility, conventional morphology (including 12 sperm anomalies), strict criteria sperm morphology analysis (SCSMA) and hypoosmotic swelling test (HOST) were compared in oligozoospermic (< 5.0, 5.1-10.0 and 10.1-20.0 x 10(6)/mL), normozoospermic (20.1-40.0, 40.1-100.0 and 100.1-250.0 x 10(6)/mL) and polyzoospermic (> 250.0 x 10(6)/mL) semen samples from 233 suspected infertile men. RESULTS Percentage of sperm viability, category a and categories a plus b of sperm motility, oval-headed sperm, and normal-headed sperm according to SCSMA and HOST had a direct relationship with sperm counts (P < .001). Percentage of amorphous heads, pinheads, tapering and combined defects showed an inverse relationship with sperm counts (P < .001), whereas the percentage of large-headed sperm was highest in semen with > 40.0 x 10(6)/mL (P = .003) and of neck/midpiece defects was lowest in semen with < 10.0 x 10(6)/mL (P = .03). No significant differences were found in the percentage of small heads, double heads, round heads, partially elongated heads, cytoplasmic droplet and tail defects. Based on the cutoff points established previously for the sperm characteristics analyzed, normal values were found in semen with > 250.0 x 10(6)/mL (viability and motility), > 100.0 x 10(6)/mL (conventional morphology) and > 40.0 x 10(6)/mL (SCSMA and HOST). CONCLUSION The incidence of defective spermatozoa is lowest in semen with the highest sperm count. However, sperm abnormalities that affect male fertility may be detected at any level of sperm density. The data indicate that an increase in any sperm abnormality should be regarded as a possible cause of decreased fertility.
Authenticating Ancient Human Mitochondrial DNA

The use of ancient DNA techniques in human studies has been hampered by problems of contamination with modern human DNA. The main problem has been that the object of study belongs to the same species as the observer, and the complete elimination of the contamination risk is seemingly unlikely. Contamination has even been detected in the most specialized laboratories in this field. In these kinds of studies it is therefore very important to detect contamination and to distinguish contaminants from authentic results. Here, we report the use of a strategy to authenticate the identity of ancient mitochondrial DNA (mtDNA), based on the previously established relationship between D-loop sequence substitutions and haplogroup-specific restriction site changes. Forty-four individuals from a 16th-century necropolis were analyzed, from which 28 control region sequences were obtained. These sequences were preclassified into haplogroups, according to the observed motifs. Subsequently, the DNA extracts from which the sequences were obtained, along with independent extracts of subsets of the same individuals, were subjected to restriction fragment length polymorphism (RFLP) analysis to compare and corroborate the results. Using this approach, 24 sequences were authenticated, while two were discarded because of result mismatches. The final distribution of the haplogroups in the sample, and the differences in the sequences, are two additional criteria of authentication.
β-Arrestin inhibits NF-κB activity by means of its interaction with the NF-κB inhibitor IκBα

In addition to their roles in desensitization and signaling of seven-membrane-spanning receptors, β-arrestins have been more recently implicated in regulating non-seven-membrane-spanning receptor pathways. By using a yeast two-hybrid screen, we identified the inhibitor of NF-κB, IκBα, as a binding partner of β-arrestin 1. Both β-arrestin 1 and 2 interact with IκBα in transfected cells as assessed by immunoprecipitation experiments. Additionally, upstream kinases known to regulate the function of IκBα, such as IκB kinase α and β and NF-κB-inducing kinase, were also shown to interact with β-arrestin. Overexpression of either β-arrestin 1 or β-arrestin 2 led to marked inhibition of NF-κB activity, as measured by reporter gene activity. Inhibition of NF-κB activity was independent of the type of stimulus used for NF-κB activation. Conversely, suppression of β-arrestin 1, but not β-arrestin 2, expression by using RNA interference led to a 3-fold increase in tumor necrosis factor-stimulated NF-κB activity as measured by NF-κB mobility-shift analysis. These data uncover a role of β-arrestins in the regulation of NF-κB-mediated gene regulation.
Position-, rotation-, scale-, and orientation-invariant multiple object recognition from cluttered scenes

A method of detecting target objects in still images despite any kind of geometrical distortion is demonstrated. Two existing techniques are combined, each one capable of creating invariance to various types of distortion of the target object. A maximum average correlation height (MACH) filter is used to create invariance to orientation and gives good tolerance to background clutter and noise. A log r- mapping is employed to give invariance to in-plane rotation and scale by transforming rotation and scale variations of the target object into vertical and horizontal shifts. The MACH filter is trained on the log r- map of the target for a range of orientations and applied sequentially over regions of interest in the input image. Areas producing a strong correlation response can then be used to determine the position, in-plane rotation, and scale of the target objects in the scene.
Predictors of Suggestibility and False-Memory Production in Young Adult Women

Recent controversy over memories retrieved in therapy has highlighted the importance of increasing our understanding of individual differences in suggestibility and false-memory production. The purpose of this laboratory study was to assess the ability of several clinically relevant variables (acquiescence, self-esteem, and negative affect) to predict the tendency to yield to suggestive questioning, to alter responses in the face of interpersonal criticism, or to produce false memories (in this study, false recall of implied words). Results indicated that acquiescence significantly predicted suggestibility, as did competence self-esteem scores, but global self-esteem and negative affect scores did not. False-memory production (i.e., false recall of implied words) was associated with higher levels of both acquiescence and negative affect, but the tendency to alter responses after criticism was not significantly predicted by any variable.
Treatment of 200 locally advanced (stage III) pancreatic adenocarcinoma patients with irreversible electroporation: safety and efficacy.

OBJECTIVES Ablative therapies have been increasingly utilized in the treatment of locally advanced pancreatic cancer (LAPC). Irreversible electroporation (IRE) is an energy delivery system, effective in ablating tumors by inducing irreversible membrane destruction of cells. We aimed to demonstrate efficacy of treatment with IRE as part of multimodal treatment of LAPC. METHODS From July 2010 to October 2014, patients with radiographic stage III LAPC were treated with IRE and monitored under a multicenter, prospective institutional review board-approved registry. Perioperative 90-day outcomes, local failure, and overall survival were recorded. RESULTS A total of 200 patients with LAPC underwent IRE alone (n = 150) or pancreatic resection plus IRE for margin enhancement (n = 50). All patients underwent induction chemotherapy, and 52% received chemoradiation therapy as well for a median of 6 months (range, 5-13 months) before IRE. IRE was successfully performed in all patients. Thirty-seven percent of patients sustained complications, with a median grade of 2 (range, 1-5). Median length of stay was 6 days (range, 4-36 days). With a median follow-up of 29 months, 6 patients (3%) have experienced local recurrence. Median overall survival was 24.9 months (range: 4.9-85 months). CONCLUSIONS For patients with LAPC (stage III), the addition of IRE to conventional chemotherapy and radiation therapy results in substantially prolonged survival compared with historical controls. These results suggest that ablative control of the primary tumor may prolong survival.
Application of two bicistronic systems involving 2A and IRES sequences to the biosynthesis of carotenoids in rice endosperm.

Coordination of multiple transgenes is essential for metabolic engineering of biosynthetic pathways. Here, we report the utilization of two bicistronic systems involving the 2A sequence from the foot-and-mouth disease virus and the internal ribosome entry site (IRES) sequence from the crucifer-infecting tobamovirus to the biosynthesis of carotenoids in rice endosperm. Two carotenoid biosynthetic genes, phytoene synthase (Psy) from Capsicum and carotene desaturase (CrtI) from Pantoea, were linked via either the synthetic 2A sequence that was optimized for rice codons or the IRES sequence under control of the rice globulin promoter, generating PAC (Psy-2A-CrtI) and PIC (Psy-IRES-CrtI) constructs, respectively. The transgenic endosperm of PAC rice had a more intense golden color than did PIC rice, demonstrating that 2A was more efficient than IRES in coordinating gene expression. The 2A and IRES constructs were equally effective in driving transgene transcription. However, immunoblot analysis of CRTI, a protein encoded by the downstream open reading frame of the bicistronic constructs, revealed that 2A was ninefold more effective than IRES in driving translation. The PAC endosperms accumulated an average of 1.3 μg/g of total carotenoids, which was ninefold higher than was observed for PIC endosperms. In particular, accumulation of β-carotene was much higher in PAC endosperms than in PIC endosperms. Collectively, these results demonstrate that both 2A and IRES systems can coordinate the expression of two biosynthetic genes, with the 2A system exhibiting greater efficiency. Thus, the 2A expression system described herein is an effective new tool for multigene stacking in crop biotechnology.
ASCLS Continues Collaborative Efforts to Address Laboratory Reimbursement and Workforce Issues

The theme of recent Washington Beat articles has been the Medicare Clinical Laboratory Competitive Bidding Project. This issue continues to “top” the list of legislative and regulatory issues as implementation of the demonstration project in the San Diego Metropolitan Statistical Area continues. Three San Diego-area laboratories have filed a lawsuit seeking to block the demonstration project on the grounds that the US Department of Health and Human Services failed to comply with the federal Administrative Procedure Act, failed to protect small businesses, and established a program that threatened irreparable injury to laboratories in the designated area (Sharp Healthcare v. Leavitt, S.D.Cal. No.08 CV 0170, filed 1/29/08). The American Society for Clinical Laboratory Science (ASCLS), along with the other members of the Clinical Laboratory Coalition (CLC), are supporting this lawsuit. In addition, ASCLS and other CLC member organizations continue to lobby for the passage of HR 3453 and S. 2099, bills that have been introduced to repeal the Medicare competitive bidding project for laboratory services. As efforts continue in Washington DC to address the ongoing threats to appropriate reimbursement for clinical laboratory services, another critical issue is impacting the practice of clinical laboratory science—the increasing shortage of qualified practitioners. Although the criticality of the shortage varies geographically, there is increasing concern among employers, educators, professional associations, and policy makers that the shortage will continue to worsen. The US Bureau of Labor and Statistics projects a need of approximately 150,000 new practitioners per year through 2014. Accredited educational programs are currently graduating…
Earth System Science for Global Sustainability: Grand Challenges

Progress in understanding and addressing both global environmental change and sustainable development requires better integration of social science research. Tremendous progress has been made in understanding the functioning of the Earth system and, in particular, the impact of human actions (1). Although this knowledge can inform management of specific features of our world in transition, societies need knowledge that will allow them to simultaneously reduce global environmental risks while also meeting economic development goals. For example, how can we advance science and technology, change human behavior, and influence political will to enable societies to meet targets for reductions in greenhouse gas emissions to avoid dangerous climate change? At the same time, how can we meet needs for food, water, improved health and human security, and enhanced energy security? Can this be done while also meeting the United Nations Millennium Development Goals of eradicating extreme poverty and hunger and ensuring ecosystem integrity?