gebhart/patrepeval huggingface dataset:
A model for Batten disease protein CLN3: Functional implications from homology and mutations (1996)

In an attempt to understand the molecular nature of Batten disease, we have examined the amino acid sequence of the affected CLN3 gene product (The International Batten Disease Consortium (1995) Cell 82, 949-957) and the site-specific mutations which give rise to the biological defect. Homology searches and molecular modeling have led to the development of a model for the folding and disposition of the protein, possibly within a mitochondrial membrane. High homology with a yeast protein of unknown function suggests a strong evolutionary conservation of function. We speculate that a possible role for the protein may be in chaperoning the folding/unfolding or assembly/ disassembly of other proteins, specifically subunit c of the mitochondrial ATP synthase complex.
The Etiology of Idiopathic Scoliosis (1977)

A multiple-factor approach to the puzzling diagnosis of idiopathic scoliosis is presented in an effort to shed some light on the ever-pervasive shadows of the unknown. Each factor, i.e., nutrition, hormonal influence, genetic tendency, and spinal mechanics, is discussed in detail and with excerpts and summaries from substantive recent literature are presented. Research in molecular chemistry, enzymes, coenzymes, genes, proteins, hormones, etc., at last is beginning to reveal secrets to those who have persevered in the laboratory. It would appear that a relatively minor deficiency in the disk collagen can cause the idiopathic scoliotic development in the spine. A nutritional deficit during the vulnerable growing years (hormonal influence) may initiate the scoliotic process, with the genetic tendency being a recessive factor. Thereafter, given the initial deficit, the spine has no choice--it must react to force, time and direction (mechanics of the spine)--and ultimately produce scoliosis.
Atrial natriuretic factor has a direct, prostaglandin-independent action on kidneys (1982)

Intravenous injection of a saline extract of lyophilized rat atrial myocardium into anesthetized rats caused a massive diuresis and natriuresis of short duration. There was also a significant increase in potassium excretion and a fall in urine osmolality. There were no significant changes in solute-free water reabsorption, glomerular filtration rate, renal plasma flow, or filtration fraction as measured by conventional clearance methods. Mean arterial pressure was significantly reduced during the natriuretic response. The natriuretic and diuretic response was not blocked by inhibition of prostaglandin synthesis with aspirin and indomethacin. Infusion of a small amount of atrial extract directly into the left kidney resulted in a natriuretic and diuretic response which was predominantly localized to the left kidney. It is concluded that saline extracts of rat atrial myocardium contain a potent natriuretic substance which acts directly on kidneys by a mechanism which does not depend upon increased synthesis of prostaglandins.
Fundamental limits on the frequency instabilities of quartz crystal oscillators (2002)

The frequency instabilities of precision bulk acoustic wave (BAW) quartz crystal oscillators, and the contributions from the instabilities of resonators, sustaining circuits, and ovens, are reviewed. The fundamental limits on the achievable frequency stabilities, and the degree to which the fundamental limits have been approached to date are examined. Included are the instabilities as a function of time, temperature, acceleration, ionizing radiation, electromagnetic fields, humidity, atmospheric pressure, power supply and load impedance. Most of the fundamental limits are zero or negligibly small, a few are finite. The authors speculate about the progress which may be achievable in the future with respect to approaching the fundamental limits. Suggestions are provided about the paths that may lead to significant stability improvements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Crystal structure of human CD1e reveals a groove suited for lipid-exchange processes (2011)

CD1e is the only human CD1 protein existing in soluble form in the late endosomes of dendritic cells, where it facilitates the processing of glycolipid antigens that are ultimately recognized by CD1b-restricted T cells. The precise function of CD1e remains undefined, thus impeding efforts to predict the participation of this protein in the presentation of other antigens. To gain insight into its function, we determined the crystal structure of recombinant CD1e expressed in human cells at 2.90-Å resolution. The structure revealed a groove less intricate than in other CD1 proteins, with a significantly wider portal characterized by a 2 Å-larger spacing between the α1 and α2 helices. No electron density corresponding to endogenous ligands was detected within the groove, despite the presence of ligands unequivocally established by native mass spectrometry in recombinant CD1e. Our structural data indicate that the water-exposed CD1e groove could ensure the establishment of loose contacts with lipids. In agreement with this possibility, lipid association and dissociation processes were found to be considerably faster with CD1e than with CD1b. Moreover, CD1e was found to mediate in vitro the transfer of lipids to CD1b and the displacement of lipids from stable CD1b-antigen complexes. Altogether, these data support that CD1e could have evolved to mediate lipid-exchange/editing processes with CD1b and point to a pathway whereby the repertoire of lipid antigens presented by human dendritic cells might be expanded.
Electrocardiograms of Collegiate Football Athletes (2009)

Abnormal resting ECG findings are common in a sample of collegiate football athletes, exceeding the rate expected for their age, and are more frequent in African-American athletes as compared with Caucasian athletes.
Trace Elements and Cardiovascular Diseases (1996)

The relation between trace elements and human health has been scarcely studied. With respect to cardiovascular diseases and hypertension attention has mostly focused on arsenic, cobalt, copper, chromium, fluorine, manganese, vanadium, zinc, selenium, silicon, cadmium, and lead. Environmental contamination can influence organ concentrations through long-term, low-level effects. This article reviews the present knowledge obtained by epidemiological, biochemical and cell biological studies. Attention is paid to interpretation problems due to the complexity of biochemical interactions with proteins of various sorts which determine metabolic processes and to the occurrence of detoxification mechanisms in which trace elements interact. This can also lead to strong variations in individual vulnerability. In general, the elements selenium, copper, zinc, chromium, and manganese seem to counteract the development of cardiovascular diseases, whereas cadmium and may be lead seem to stimulate it. Effects of arsenic, silicon and fluorine are unclear and for cobalt absent. The intensity of these effects on public health is difficult to measure, but is as yet probably limited except in extra-ordinary situations.
High frequency/high dynamic range CMOS VGA (2000)

A novel CMOS variable gain amplifier (VGA) with high frequency and high dynamic range is proposed. The VGA has a controllable gain range of –50 dB – +50 dB which can be controlled by adjusting the external voltage as well as an enhanced operating frequency range up to 200 MHz. It is fabricated using 0.35 µm CMOS technology and has a core area of 580 × 660 µm.
Relationship Between Total and Lipid-bound Serum Sialic Acid and Some Tumor Markers (2005)

Background: Increased levels of total and lipid-associated sialic acid (TSA and LASA) have been reported in the sera of patients with benign or malignant tumors and also could be regarded as newly important clinical criteria for the diagnosis of cancer. This study has investigated the differences of TSA and LASA contents between cancer patients and healthy individuals and evaluated their correlations between TSA and LASA with some tumor markers in different types of cancer. Methods: 35 patients with histopathologically confirmed cancers and 32 healthy individuals participated in the study. Tumor markers in serum including CEA, CA15-3, CA19-9 and CA-125 were measured using ELISA. TSA and LASA were quantified using spectrophotometric methods of Erlich and Katopodis respectively and non-parametric tests were used for statistical analysis. Results: The median (range) obtained for TSA in healthy and cancer patients were 83.6 (59.0-106.2) and 119.5 (84.7-205.8) mg/dl respectively and the difference was statistically significant (P<0.001). The corresponding values for LASA content of serum in healthy and cancer patients were 16.9 (13.3-20.7), and 31.0 (15.0-50.3) mg/dl. Statistical analysis showed significant differences in LASA content between these two groups (P<0.001). A positive correlation coefficient was obtained between TSA, LASA and different tumor markers. Conclusion: The significant correlation between TSA, LASA and different tumor markers in cancer patients indicated that they could be used as diagnostic criteria. However, due to their lack of specificity, they may support the presence of tumor markers in different malignancies and be helpful in relation to therapy and monitoring of patients.
Promotion of daunorubicin uptake and toxicity by the calcium antagonist tiapamil and its analogs. (1985)

Studies were performed with the anthracycline-responsive P388 murine leukemia cell line, and with P388/ADR, a subline selected for doxorubicin resistance. In the P388/ADR cell line, the observed 100-fold daunorubicin resistance is associated with an outward drug transport system which can be inhibited by several calcium antagonists, eg, verapamil and nifedipine. An examination of compounds related to tiapamil, a verapamil analog, has identified a structure which is tenfold more effective than verapamil at potentiating anthracycline accumulation and responsiveness in P388/ADR cells. At no nontoxic level of any calcium antagonist examined was it possible to wholly reverse the degree of daunorubicin resistance found in the P388/ADR cell line.
The Human CLN2 Protein/Tripeptidyl-Peptidase I Is a Serine Protease That Autoactivates at Acidic pH (2001)

The CLN2 gene mutated in the fatal hereditary neurodegenerative disease late infantile neuronal ceroid lipofuscinosis encodes a lysosomal protease with tripeptidyl-peptidase I activity. To understand the enzymological properties of the protein, we purified and characterized C-terminal hexahistidine-tagged human CLN2p/tripeptidyl-peptidase I produced from insect cells transfected with a baculovirus vector. The N terminus of the secreted 66-kDa protein corresponds to residue 20 of the primary CLN2 gene translation product, indicating removal of a 19-residue signal peptide. The purified protein is enzymatically inactive; however, upon acidification, it is proteolytically processed and concomitantly acquires enzymatic activity. The N terminus of the final 46-kDa processed form (Leu196) corresponds to that of mature CLN2p/tripeptidyl-peptidase I purified from human brain. The activity of the mature enzyme is irreversibly inhibited by the serine esterase inhibitor diisopropyl fluorophosphate, which specifically and stoichiometrically reacts with CLN2p/tripeptidyl-peptidase I at Ser475, demonstrating that this residue represents the active site nucleophile. Expression of wild type and mutant proteins in CHO cells indicate that Ser475, Asp360, Asp517, but not His236 are essential for activity. These data indicate that the CLN2 gene product is synthesized as an inactive proenzyme that is autocatalytically converted to an active serine protease.
The Targets of Currently Used Antibacterial Agents: Lessons for Drug Discovery (2007)

Based on the mode of action of antibacterial drugs currently used, targets can be defined as distinct cellular constituents such as enzymes, enzyme substrates, RNA, DNA, and membranes which exhibit very specific binding sites at the surface of these components or at the interface of macromolecular complexes assembled in the cell. Intriguingly, growth inhibition or even complete loss of bacterial viability is often the result of a cascade of events elicited upon treatment with an antibacterial agent. In addition, their mode of action frequently involves more than one single target. A comprehensive description of the targets exploited so far by commercialized antibacterial agents, including anti-mycobacterial agents, is given. The number of targets exploited so far by commercial antibacterial agents is estimated to be about 40. The most important biosynthetic pathways and cellular structures affected by antibacterial drugs are the cell wall biosynthesis, protein biosynthesis, DNA per se, replication, RNA per se, transcription and the folate biosynthetic pathway. The disillusionment with the genomics driven antibacterial drug discovery is a result of the restrictive definition of targets as products of essential and conserved genes. Emphasis is made to not only focus on proteins as potential drug targets, but increase efforts and devise screening technologies to discover new agents interacting with different RNA species, DNA, new protein families or macromolecular complexes of these constituents.
Fabrication of T gate structures by nanoimprint lithography (2001)

Nanoimprint lithography is capable of patterning substrates with high definition patterns at relatively high patterning speeds. In this article we describe the fabrication of high resolution “T” gate resist profiles by imprint lithography. The fabrication of high resolution stamping tools and the imprinting process itself are critical to the success or failure of this technique and they are described in the article. Two different techniques were used to fabricate stamping tools. The first involved pattern definition by high resolution electron beam lithography followed by electroforming. The second involved pattern definition by electron beam lithography followed by a two stage silicon etching process. Imprinted T gate resist profiles with footwidths less than 100 nm in length were obtained on gallium arsenide substrates for the purpose of producing metallized gates for a self-aligned gate process.
美国民俗学／非物质文化遗产保护中的“本真性”问题 (2015)

在美国，“本真性”这一概念是一个精致而复杂的建构，是民俗工作和文化自身中定义合法性的核心。假定“本真性”是民俗学理性研究数十载的成果以及学术推论，它也可被视作一些民俗学者及其拥护者发明和部署的一种策略，以便将物质素材、社区和与中产阶级的精致性、政治意识形态、商业实体和大众传播机制相关的实践活动进行恰当的定位。和直观的或“自然的”不同，本真性本身是人为制造的。尽管这一概念符合一些学者和活动家的需要，但是当被僵化地使用时，本真性也对功能性的概念提出质疑，即传统行为实际上如何为个人和社区服务。在美国语境中，什么是“本真性”明确和暗含的标识？美国的本真性概念是否太过狭隘和条框化？在面对2l世纪的文化保护与实践问题时，在全世界对非物质文化遗产的标识有一种共识时，美国民俗学者是否能够或者是否应该找到办法调整本真性的理念？
Crosslinking effect on polydimethylsiloxane elastic modulus measured by custom‐built compression instrument (2014)

ABSTRACT A macroscopic compression test utilizing a simple custom‐built instrument was employed to measure polydimethylsiloxane (PDMS) elastic modulus. PDMS samples with varying crosslinking density were prepared with the elastomer base to the curing agent ratio ranging from 5 : 1 to 33 : 1. The PDMS network elastic modulus varied linearly with the amount of crosslinker, ranging from 0.57 MPa to 3.7 MPa for the samples tested. PDMS elastic modulus in MPa can be expressed as 20 MPa/PDMS base to curing agent ratio. This article describes a simple method for measuring elastic properties of soft polymeric materials. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 41050.
Effect of experimental parameters on the formation of chitosan–poly(acrylic acid) nanofibrous scaffolds and evaluation of their potential application as DNA carrier (2009)

Abstract Gene delivery from tissue engineering scaffolds has demonstrated the ability to promote gene transfer and stimulate new tissue formation. In this article we report a novel nanofibrous scaffold based on polyelectrolyte complexes as a vehicle for delivery of DNA. When polycation chitosan (CS) was dropped into polyanion poly(acrylic acid) (PAA) suspension and freeze‐dried, CS‐PAA nanofibrous scaffold with diverse microstructure would be formed under different experimental conditions. The nanofiber size was affected by the CS molecular weight, the concentration of CS, the volume ratio of CS to PAA, the reaction temperature, the incubation time, and the final pH of the suspension as well. By using adipic acid as branch promoter, adjusting the pH value of the CS solution to 3, and then dropping CS into the PAA solution at a ratio of 3 : 1, a nanofibrous structure with average diameter 140 nm is obtained after the suspension is freeze‐dried. These nanofibrous scaffolds were nontoxic and can encapsulate plasmid DNA very well. Transgenic expression in human dermal fibroblasts seeded on the nanofibrous scaffolds was significant after 14 days compared to lipofectamine controls. This result indicates that CS‐PAA nanofibrous scaffold have favorable characteristics for nonviral gene delivery to mammalian cell, and have the potential to enhance gene transfer in tissue engineering. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Electronic payment systems and security (2005)

Electronic payment is the most important activity in e-commerce. In this paper an overview of electronic payment systems is given. The main challenge in contemporary electronic payment systems is its security. Having this in mind, in this paper the security problems are described and possible solutions are given.
Path-velocity decomposition revisited and applied to dynamic trajectory planning (2002)

Dynamic trajectory planning is addressed. The case of a car-like robot, A, with bounded velocity and acceleration, moving in a dynamic workspace W=R/sup 2/ is considered. The concept of adjacent paths is introduced, and used within a novel motion planning schema which operates in two complementary stages, paths-planning and trajectory-planning. In the paths-planning stage, a set of adjacent paths, one of which leads A to its goal, are computed. These paths are collision-free with the stationary obstacles and respect A's kinematic constraints. In the trajectory-planning stage, knowing that A is able to shift from one path to an adjacent one freely, the motion of A along and between these paths is determined so as to avoid any collision with the moving obstacles while respecting A's dynamic constraints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
COMPARISON OF CYANAMIDE AND PLACEBO IN THE TREATMENT OF ALCOHOL DEPENDENCE OF ADOLESCENTS (2003)

Cyanamide seems to be an effective and well tolerated pharmacological adjunct to psychosocial and behavioural treatment programmes for the treatment of some adolescent alcohol-dependent patients. Because of reported hepatotoxic, haematological and dermatological side effects, patients should be observed continuously by experienced clinicians. Further studies are necessary to prove the efficacy of cyanamide in adolescents.
Healing of intrabony defects following treatment with a bovine‐derived xenograft and collagen membrane (2003)

: Within the limits of the present study, it can be concluded that: (i) at 1 year after surgery both therapies resulted in significant PD reductions and CAL gains, and (ii) treatment with BDX+collagen membrane resulted in significantly higher CAL gains than treatment with access flap surgery.
Analysis of the impact of pupil shape variation by pupil fit modeling (2010)

As K1 factor for mass-production of memory devices has been decreased to almost its theoretical limit, the process window of lithography is getting much smaller and the production yield has become more sensitive to even small variations of the process in lithography. So it is necessary to control the process variations more tightly than ever. In mass-production, it is very hard to extend the production capacity if the tool-to-tool variation of scanners and/or scanner stability through time is not minimized. One of the most critical sources of variation is the illumination pupil. So it is critical to qualify the shape of pupils in scanners to control tool-to-tool variations. Traditionally, the pupil shape has been analyzed by using classical pupil parameters to define pupil shape, but these basic parameters, sometimes, cannot distinguish the tool-to-tool variations. It has been found that the pupil shape can be changed by illumination misalignment or damages in optics and theses changes can have a great effect on critical dimension (CD), pattern profile or OPC accuracy. These imaging effects are not captured by the basic pupil parameters. The correlation between CD and pupil parameters will become even more difficult with the introduction of more complex (freeform) illumination pupils. In this paper, illumination pupils were analyzed using a more sophisticated parametric pupil description (Pupil Fit Model, PFM). And the impact of pupil shape variations on CD for critical features is investigated. The tool-to-tool mismatching in gate layer of 4X memory device was demonstrated for an example. Also, we interpreted which parameter is most sensitive to CD for different applications. It was found that the more sophisticated parametric pupil description is much better compared to the traditional way of pupil control. However, our examples also show that the tool-to-tool pupil variation and pupil variation through time of a scanner can not be adequately monitored by pupil parameters only, The best pupil control strategy is a combination of pupil parameters and simulated CD using measured illumination pupils or modeled pupils.
Functional Characterization of a Non-AUUUA AU-Rich Element from the c-<i>jun</i> Proto-Oncogene mRNA: Evidence for a Novel Class of AU-Rich Elements (1996)

AU-rich RNA-destabilizing elements (AREs) found in the 3' untranslated regions of many labile mRNAs encoding proto-oncoproteins and cytokines generally contain (i) one or more copies of the AUUUA pentanucleotide and (ii) a high content of uridylate and sometimes also adenylate residues. Recently, we have identified a potent ARE from the 3' untranslated region of c-jun proto-oncogene mRNA that does not contain the AUUUA motif. In an attempt to further our understanding of the general principles underlying mechanisms by which AREs direct rapid and selective mRNA degradation, in this study we have characterized the functionally important structural features and properties of this non-AUUUA ARE. Like AUUUA-containing AREs, this non-AUUUA ARE directs rapid shortening of the poly(A) tail as a necessary first step for mRNA degradation. It can be further dissected into three structurally and functionally distinct regions, designated domains I, II, and III. None of three domains alone is able to significantly destabilize the stable beta-globin mRNA. The two unlinked domains, I and III, together are necessary and sufficient for specifying the full destabilizing function of this non-AUUUA ARE. Domain II appears functionally dispensable but can partially substitute for domain I. Domain swaps made between the c-jun non-AUUUA and the c-fos AUUUA-containing AREs reveal that the two AREs, while sharing no sequence homology, appear to contain sequence domains that are structurally distinct but functionally overlapping and exchangeable. These data support the idea that the ultimate destabilizing function of an individual ARE is determined by its own unique combination of structurally distinct and functionally interdependent domains. Our polysome profile studies show tha the destabilizing function of the c-jun non-AUUUA ARE does not require any active transit by ribosomes of the mRNA bearing it, further corroborating that the destabilizing function of AREs is not tightly coupled to ongoing translation by ribosomes. Moreover, unlike AUUUA-containing AREs, the c-jun ARE is insensitive to blockage of its effects by addition of transcription inhibitors. Thus, our data provide further evidence for the existence of a novel class of ARE with unique properties.