gebhart/patrepeval huggingface dataset:
AP-1 and KIF13A coordinate endosomal sorting and positioning during melanosome biogenesis (2009)

Specialized cell types exploit endosomal trafficking to deliver protein cargoes to cell type-specific lysosome-related organelles (LROs), but how endosomes are specified for this function is not known. In this study, we show that the clathrin adaptor AP-1 and the kinesin motor KIF13A together create peripheral recycling endosomal subdomains in melanocytes required for cargo delivery to maturing melanosomes. In cells depleted of AP-1 or KIF13A, a subpopulation of recycling endosomes redistributes to pericentriolar clusters, resulting in sequestration of melanosomal enzymes like Tyrp1 in vacuolar endosomes and consequent inhibition of melanin synthesis and melanosome maturation. Immunocytochemistry, live cell imaging, and electron tomography reveal AP-1- and KIF13A-dependent dynamic close appositions and continuities between peripheral endosomal tubules and melanosomes. Our results reveal that LRO protein sorting is coupled to cell type-specific positioning of endosomes that facilitate endosome-LRO contacts and are required for organelle maturation.
Post CMOS Compatible Aluminum Nitride Filters MEMS Filters and Resonant Sensors. (2007)

Abstract not provided.
Potential of Surgery for Curing Type 2 Diabetes Mellitus (2002)

Gastric bypass and biliopancreatic diversion seem to achieve control of diabetes as a primary and independent effect, not secondary to the treatment of overweight. Although controlled trials are needed to verify the effectiveness on nonobese individuals, gastric bypass surgery has the potential to change the current concepts of the pathophysiology of type 2 diabetes and, possibly, the management of this disease.
Omalizumab therapy in three patients with chronic autoimmune urticaria (2010)

Chronic urticaria is a common skin disease. In about 45&#x0025; of patients the cause is an autoantibody directed at the &#945;-subunit of the high-affinity IgE receptor (chronic autoimmune urticaria; CAU). Omalizumab is a monoclonal anti-IgE antibody that has a proven role in the treatment of various allergic diseases. We gave omalizumab once every month for 16 weeks to three patients that were refractory to standard treatment, including high doses of antihistamines, leukotriene receptor antagonist, and corticosteroid. There was dramatic improvement in the primary efficacy variable-the change in mean urticaria activity score (UAS) from baseline (i.e., the average over the first 4-week period before omalizumab) to the final 4-week period of omalizumab treatment. There was improvement in the secondary efficacy variables, which included change from baseline in interference with sleep, interference with daily activities, daily diary record of urticaria signs and symptoms based on a scoring system, and rescue medication use. These improvements persisted for 12 weeks after discontinuation of the drug. Omalizumab may have a role in treating refractory cases of CAU.
Glutamate, Dopamine, and Schizophrenia (2003)

The fundamental pathological process(es) associated with schizophrenia remain(s) uncertain, but multiple lines of evidence suggest that this condition is associated with (1) excessive stimulation of striatal dopamine (DA) D2 receptors, (2) deficient stimulation of prefrontal DA D1 receptors and, (3) alterations in prefrontal connectivity involving glutamate (GLU) transmission at N-methyl-d-aspartate (NMDA) receptors. This chapter first briefly discusses the current knowledge status for these abnormalities, with emphasis on results derived from clinical molecular imaging studies. The evidence for hyperstimulation of striatal D2 receptors rests on strong pharmacological evidence and has recently received support from brain imaging studies. The hypothesis of deficient prefrontal cortex (PFC) D1 receptor stimulation is almost entirely derived from preclinical studies. Preliminary imaging data compatible with this hypothesis have recently emerged. The NMDA hypofunction hypothesis originates mainly from indirect pharmacological data. The interactions between DA and GLU systems relevant to schizophrenia are then reviewed. Animal and imaging data supporting the general model that the putative DA imbalance in schizophrenia (striatal excess and cortical deficiency) might be secondary to NMDA hypofunction in the PFC and its connections are presented. Equally important are the potential consequences of this DA imbalance for NMDA function in the striatum and the cortex, which are subsequently discussed. In conclusion, it is proposed that schizophrenia is associated with strongly interconnected abnormalities of GLU and DA transmission: NMDA hypofunction in the PFC and its connections might generate a pattern of dysregulation of DA systems that, in turn, further weakens NMDA-mediated connectivity and plasticity.
Expression and prognostic roles of beta-catenin in hepatocellular carcinoma: correlation with tumor progression and postoperative survival. (2002)

Our present data suggest that beta-catenin plays important roles in promoting tumor progression by stimulating tumor cell proliferation and reducing the activity of cell adhesion systems and is associated with a poor prognosis, especially in patients with poorly differentiated HCCs.
Nucleotide Sequence of Cauliflower Mosaic Virus Isolate NY8153 (1992)

Cauliflower mosaic virus (CaMV) is the type member of the caulimoviruses, a group of plant viruses with double- stranded DNA as their genetic material.Caulimoviruses have a restricted host range, usually one or two families.CaMV mainly infects members of the Crucifereae and Solanaceae.The details of CaMV molecular biology have been extensively reviewed (2, 4).The double-stranded genome of CaMV con- tains three discontinuities (gaps), one in the minus (tran- scribed) strand and two in the plus strand.There are two major transcripts of CaMV (Table I).The larger transcript (35S) has eight tightly packed potential open reading frames and a noncoding region of approximately 700 bp.The known functions of five genes are shown in Table I.Several CaMV isolates are known and the genomes of some have been sequenced completely.Here, we report the nucleotide se- quence of CaMV isolate NY8153 (Fig. 1).Disease symptoms induced on turnip by NY8153 have been described (6).
Dissecting the hemagglutinin head and stalk-specific IgG antibody response in healthcare workers following pandemic H1N1 vaccination (2016)

Traditionally, neutralising antibodies that are directed to the major surface glycoprotein hemagglutinin (HA) head domain are measured as surrogate correlates of protection against influenza. In addition to neutralization, hemagglutinin-specific antibodies may provide protection by mediating antibody-dependent cellular cytotoxicity (ADCC). During the 2009 pandemic, vaccination induced HA-specific antibodies that were mostly directed to the conserved HA stalk domain. However, the protective role of these antibodies has not been investigated in detail. We quantified the HA head and stalk-specific antibodies, their avidity, ability to neutralise virus and activate natural killer cells in an ADCC assay. We analyzed sera obtained from 14 healthcare workers who had low hemagglutination inhibition (HI) antibody titres at 3 months after pandemic H1N1 vaccination as well as from 22 controls. Vaccination resulted in a HA stalk dominant antibody response in both low responders and controls. Revaccination of low responders, 5 months later, resulted in a boost in antibodies, with HA head-specific antibodies dominating the response. Comparative analysis of head and stalk antibody avidities revealed that stalk-specific antibodies were qualitatively superior. Furthermore, stalk-specific antibodies mediated virus neutralization and had significantly higher ADCC activity than head-specific antibodies. Despite the head and stalk-specific antibodies being lower in low responders, they had comparable antibody avidity, ADCC functionality and neutralising capacity to those of controls who had high HI titres post-vaccination. Thus, our study has demonstrated that HA stalk-specific antibodies may have an important role in protection through neutralization and ADCC in low responders who do not maintain seroprotective HI antibodies.
Naturally occurring circular proteins: distribution, biosynthesis and evolution (2010)

Circular proteins, i.e., proteins with a backbone comprised of a continuous and seamless circle of amino acids, have been discovered over the last 15 years in bacteria, plants, fungi and animals. They function as defence tools in the organisms in which they are expressed and are exceptionally stable. The cyclotides are the largest known family of circular proteins and are expressed by plants of the Violaceae (violet), Rubiaceae (coffee) and Cucurbitaceae (cucurbit) families, where they have a role in plant defence against insect predation. So far there are fewer examples of cyclic peptides in bacteria or animals but we suggest that cyclic peptides are an underdiscovered class of molecules and that many more will be discovered in the near future. There is much interest in understanding the mechanism of cyclization of circular proteins and the role of the cyclic backbone in defining structure and activity. In this review, the families of ribosomally synthesized cyclic proteins reported to date are described and their common features are examined, providing information on their distribution, biosynthesis and evolution. The unusual structure of circular proteins confers them with high stability, and makes them very interesting as scaffolds for drug design, and this has led to the re-engineering of linear proteins to stabilise them and use them for such applications.
Prognostic Implications of Chemoresistance-Sensitivity Assays for Colorectal and Appendiceal Cancer (1995)

A major problem with pharmacologic treatments for cancer is the unpredictable nature of the clinical response. Therefore, many patients are treated but few benefit from chemotherapy. Selection of patients for drug treatment would greatly benefit both responders and nonresponders. Mitomycin C (MMC) and 5-fluorouracil (5-FU) are important drugs widely used in the treatment of patients with gastrointestinal malignancies. In a prospective study, an in vitro chemoresistance-sensitivity assay (CR-SA) was performed for 95 patients at the time of surgery for peritoneal carcinomatosis from colorectal and appendiceal cancer. Following cytoreductive surgery, all of these patients had minimal-to-moderate residual disease. All patients were treated with the same chemotherapy regimen regardless of the results of the in vitro assay in the postoperative period. Clinical status of patients was correlated to the assay predictions, and the results were statistically evaluated. When resistance was correlated with outcome, there was no statistical difference. In addition, the mean percentage of growth inhibition was not increased when responders and nonresponders were compared. Finally, more patients who had > or = 95% in vitro growth inhibition of cancer did not survive than did those with < or = 95% growth inhibition. The in vitro test did not predict sensitivity or resistance to cancer when regional chemotherapy was administered in a clinical setting of peritoneal carcinomatosis.
Haplotypes of the interleukin‐4 receptor α chain gene associate with susceptibility to and severity of atopic asthma (2004)

Our data suggest that asthmatic patients with low levels of sIL-4 receptor may represent a genetically distinct subgroup of atopic asthma. TVR haplotype analyses confirm the importance of IL4R as a candidate gene for susceptibility to asthma. This finding may have implications for the understanding of the pathogenesis of asthma and possibly for the development of more specific therapies.
A 1.5nsec/2.1nsec random read/write cycle 1Mb STT-RAM using 6T2MTJ cell with background write for nonvolatile e-memories (2013)

A 1Mb STT-RAM with a 6T2MTJ cell is designed and fabricated using 90nm CMOS/MTJ process that can operate in 1.5nsec/2.1nsec random read/write cycle by adopting a background write scheme. It works around the problem of high error rate of MTJ switching in a short period of time at moderate drive current. The RAM is fast enough to be applicable to embedded memories such as L3 cache.
<title>Consistent segmentation of repeat CT scans for growth assessment in pulmonary nodules</title> (1999)

Nodule growth is a key characteristic of malignancy. The measurement of nodule diameter on chest radiographs has been unsatisfactory due to insufficient accuracy and reproducibility. Additionally, the frequent use of high resolution CT scanners has increased the detection rate of very small nodules. On one hand, the small nodules present even greater diagnostic difficulties and, on the other hand, are more frequently benign, resulting in higher rates of unnecessary surgery. In this paper we present a 3-D algorithm to improve the consistency of nodule segmentation on multiple scans. The multi-criterion, multi-scan segmentation algorithm has been developed based on the fact that a typical small pulmonary nodule has distinct difference in density at the boundary and relatively compact shape, and that other tissues in the lung do not change in size over time. Our preliminary results with in-vivo nodules have shown the potential of applying this practical 3-D segmentation algorithm to clinical settings.
The phosphatidylinositol 3'-kinase p85alpha gene is an oncogene in human ovarian and colon tumors. (2001)

Phosphatidylinositol 3'-kinases (PI3ks) are a family of lipid kinases that play a crucial role in a wide range of important cellular processes associated with malignant behavior including cell growth, migration, and survival. We have used single-strand conformational polymorphism/heteroduplex analysis to demonstrate the presence of somatic mutations in the gene for the p85alpha regulatory subunit of PI3k (PIK3R1) in primary human colon and ovarian tumors and cancer cell lines. All of the mutations lead to deletions in the inter-SH2 region of the molecule proximal to the serine608 autoregulatory site. Expression of a mutant protein with a 23 amino acid deletion leads to constitutive activation of PI3k providing the first direct evidence that p85alpha is a new oncogene involved in human tumorigenesis.
Microcalorimeters May Provide a Solution to the Big Problem of Small Contaminants (1998)

As microelectronic devices continue to shrink, submicrometer-sized contaminants pose a serious threat to semiconductor yields and performance—and thereby to the profits of the nearly $200 billion a year industry. Chemical analysis of these tiny particles can suggest remedies for avoiding contamination by helping to pinpoint its sources. One of the most successful microchemical analysis tools combines electron microscopy with spectroscopic analysis of x rays excited in the target impurity by the microscope's electron beam. Unfortunately, the choice of x-ray detector has traditionally involved a trade-off between energy resolution and speed. So the semiconductor industry—where time equals a lot of money—has often had to supplement spectrometry with educated guesswork. Now, John Martinis, Kent Irwin, Gene Hilton and David Wollman, working at the National Institute of Standards and Technology facility in Boulder, Colorado, have developed an x-ray detector that they hope will remove some of that guesswork.
Stevia (Stevia rebaudiana) a bio-sweetener: a review (2009)

Studies revealed that Stevia has been used throughout the world since ancient times for various purposes; for example, as a sweetener and a medicine. We conducted a systematic literature review to summarize and quantify the past and current evidence for Stevia. We searched relevant papers up to 2007 in various databases. As we know that the leaves of Stevia plants have functional and sensory properties superior to those of many other high-potency sweeteners, Stevia is likely to become a major source of high-potency sweetener for the growing natural food market in the future. Although Stevia can be helpful to anyone, there are certain groups who are more likely to benefit from its remarkable sweetening potential. These include diabetic patients, those interested in decreasing caloric intake, and children. Stevia is a small perennial shrub that has been used for centuries as a bio-sweetener and for other medicinal uses such as to lower blood sugar. Its white crystalline compound (stevioside) is the natural herbal sweetener with no calories and is over 100-300 times sweeter than table sugar.
Influence of Degraded Phosphatidylserine on Binding of Antiphospholipid Antibodies (1997)

Striking differences in the antiphospholipid antibody reactivity with cardiolipin, phosphatidylserine and degraded phosphatidylserine in the presence of serum proteins were observed among patients with venous thromboembolism. The analyses showed that the degradation of phosphatidylserine influences the binding of aPL in in vitro assays.
Making It All Compute: Busting Cultural Barriers from Egypt to the United States (2013)

Lamia Youseff, a project manager at Google, was a few years into her graduate program in computer science at the University of California, Santa Barbara (UCSB), when she suddenly noticed that she was the only female student in her advanced operating systems class. She was somewhat baffled. Her undergraduate class in computer science at The American University in Cairo had been 50% men and 50% women, and it was common for a female student to be at the top of the class. "I never realized that computer science as a field is a male-dominated field until I moved to the U.S.," she says. "Luckily," she adds, "I was the top student in that class as well."
A Modular Metadata Extraction System for Born-Digital Articles (2012)

We present a comprehensive system for extracting metadata from scholarly articles. In our approach the entire document is inspected, including headers and footers of all the pages as well as bibliographic references. The system is based on a modular workflow which allows for evaluation, unit testing and replacement of individual components. The workflow is optimized towards processing of born-digital documents, but may accept scanned document images as well. The machine-learning approaches we have chosen for solving individual tasks increase the ability to adapt to new document layouts and formats. The evaluation tests we have performed showed good results of the individual implementations and the entire metadata extraction process.
Eliminating partially-redundant array-bounds check in the Android Dalvik JIT compiler (2011)

The Android operating system has transformed the mobile software platform landscape significantly. A significant component of the Android is the Dalvik Virtual Machine (DVM) that interprets client applications' codes written in Java and compiled to dexcode. Since interpretation is inherently slow, virtual machines typically employ just-in-time (JIT) compilation. In the Froyo 2.2 release of Android, DVM added a JIT compiler that selectively compiles hot-traces to native ARM code. Some crucial optimizations such as array bounds-check optimization have been implemented in the DVM-JIT compiler. DVM implements an extension of the state-of-the-art in optimization of partially-redundant array-bounds check, which is the approach of Wurthinger et al. as implemented in Java Hot-Spot Compiler. That technique has a limitation that it can optimize bounds checks only for indices that are "iterator plus a constant". In this paper, we tackle that problem by proposing an extension that can handle indices that are "affine functions of iterators, loop-invariants and literals". Our extension is fast and is implemented into the DVM JIT compiler.
Steroid Transport, Accumulation, and Antagonism of P-Glycoprotein in Multidrug-Resistant Cells (1996)

According to multiple reports, progesterone is not transported by P-glycoprotein (Pgp), which mediates multidrug resistance through active drug efflux. However, progesterone has been shown to block Pgp- mediated efflux of other drugs. To extend these observations and to examine the effect of modulating Pgp phosphorylation, the accumulation of progesterone and 14 other steroids in untreated and calphostin C-treated multidrug-resistant human colon carcinoma SW620 Ad300 cells was compared to the accumulation in parental SW620 cells. However, the accumlation of more hydrophilic steroids was reduced by as much as 50%. Progesterone and progesterone-like compounds, however were potent inhibitors of Pgp-mediated vinblastine efflux; increased antagonism correlated with increased steroid hydrophobicity. Treatment with calphostin C, a PKC inhibitor which decreases Pgp phosphorylation, increased progesterone efflux, modulated Pgp antagonism by steroids, and inhibited photoaffinity labeling of Pgp by progesterone. These results extend previous observations that Pgp can mediate the transport of, and be antagonized by, a variety of steroids and that these properties vary with both steroid's hydrophobicity and the phosphorylated state of Pgp.
Tactile Devices To Sense Touch on a Par with a Human Finger (2008)

Our sense of touch enables us to recognize texture and shape and to grasp objects. The challenge in making an electronic skin which can emulate touch for applications such as a humanoid robot or minimally invasive and remote surgery is both in mimicking the (passive) mechanical properties of the dermis and the characteristics of the sensing mechanism, especially the intrinsic digital nature of neurons. Significant progress has been made towards developing an electronic skin by using a variety of materials and physical concepts, but the challenge of emulating the sense of touch remains. Recently, a nanodevice was developed that has achieved the resolution to decipher touch on a par with the human finger; this resolution is over an order of magnitude improvement on previous devices with a sensing area larger than 1 cm(2). With its robust mechanical properties, this new system represents an important step towards the realization of artificial touch.
Phase I study of recombinant methionyl human consensus interferon (r-metHuIFN-Con1). (1988)

Consensus interferon (r-metHuIFN-Con1) is the product of a gene constructed to code for the most frequent amino acid residues known to occur in subspecies of alpha interferons. Twenty-one patients with advanced malignancy entered this phase I trial with dosing levels of 3, 7.5, 15, 30, and 45 mcg/m2/day given intramuscularly on days 1-5 and 8-10 of each 28-day cycle. The initial dose was randomly given by intravenous, intramuscular, or subcutaneous injection to facilitate pharmacokinetic studies. Vomiting and diarrhea were dose-limiting at 45 mcg/m2/day, preventing completion of therapy. Malaise, flu-like symptoms, nausea, and headache were frequent but tolerable at a dose of 30 mcg/m2/day. Patients were able to escalate to 45 mg/m2/day, suggesting tachyphlaxis to these toxicities. The initial distribution phase (T1/2 alpha) was 4.9-9.0 minutes with a T1/2 beta of 34-415 minutes in three patients for whom sequential values could be determined. r-MetHuIFN-Con1 was absorbed after both subcutaneous and intramuscular administration. 2'5'-Synthetase levels increased following treatment, although no consistent pattern was noted. One partial response was seen in a patient with gastrointestinal carcinoma. The recommended phase II starting dose of r-metHuIFN-Con1 is 30 mg/m2/day using this schedule by any of these routes of administration.