gebhart/patrepeval huggingface dataset:
Prevention of type 1 diabetes by gene therapy (2004)

The autoimmune disease type 1 diabetes in humans and NOD mice is determined by multiple genetic factors, among the strongest of which is the inheritance of diabetes-permissive MHC class II alleles associated with susceptibility to disease. Here we examined whether expression of MHC class II alleles associated with resistance to disease could be used to prevent the occurrence of diabetes. Expression of diabetes-resistant MHC class II I-Abeta chain molecules in NOD mice following retroviral transduction of autologous bone marrow hematopoietic stem cells prevented the development of autoreactive T cells by intrathymic deletion and protected the mice from the development of insulitis and diabetes. These data suggest that type 1 diabetes could be prevented in individuals expressing MHC alleles associated with susceptibility to disease by restoration of protective MHC class II expression through genetic engineering of hematopoietic stem cells.
Learning to Rank by Maximizing AUC with Linear Programming (2006)

Area Under the ROC Curve (AUC) is often used to evaluate ranking performance in binary classification problems. Several researchers have approached AUC optimization by approximating the equivalent Wicoxon-Mann-Whitney (WMW) statistic. We present a linear programming approach similar to 1-norm Support Vector Machines (SVMs) for instance ranking by an approximation to the WMW statistic. Our formulation can be applied to nonlinear problems by using a kernel function. Our ranking algorithm outperforms SVMs in both AUC and classification performance when using RBF kernels, but curiously not with polynomial kernels. We experiment with variations of chunking to handle the quadratic growth of the number of constraints in our formulation.
Noradrenaline contractions of human prostate mediated by α<sub>1c</sub>‐(α<sub>1c</sub>‐) adrenoceptor subtype (1995)

1. The subtype of alpha 1-adrenoceptor mediating contractions of human prostate to noradrenaline was characterized by use of a range of competitive and non-competitive antagonists. 2. Contractions of the prostate to either noradrenaline (pD2 5.5), phenylephrine (pD2 5.1) or methoxamine (pD2 4.4) were unaltered by the presence of neuronal and extraneuronal uptake blockers. Noradrenaline was about 3 and 10 times more potent than phenylephrine and methoxamine respectively. Phenylephrine and methoxamine were partial agonists. 3. Pretreatment with the alkylating agent, chlorethylclonidine (10(-4M) shifted the noradrenaline concentration-contraction curve about 3 fold to the right and depressed the maximum response by 31%. This shift is 100 fold less than that previously shown to be produced by chlorethylclonidine under the same conditions on alpha 1B-adrenoceptor-mediated contractions. 4. Cumulative concentration-contraction curves for noradrenaline were competitively antagonized by WB 4101 (pA2 9.0), 5-methyl-urapidil (pA2 8.6), phentolamine (pA2 7.6), benoxathian (pA2 8.5), spiperone (pA2 7.3), indoramin (pA2 8.2) and BMY 7378 (pA2 6.6). These values correlated best with published pKi values for their displacement of [3H]-prazosin binding on membranes expressing cloned alpha 1c-adrenoceptors and poorly with values from cloned alpha 1b- and alpha 1d-adrenoceptors. 5. The good correlation between the functional data on the prostate and the binding data on the expressed alpha 1c-subtype clone for the affinities of the competitive antagonists suggests that they are the same subtype. As the expressed alpha 1c-adrenoceptor clone corresponds to the alpha 1A-adrenoceptor expressed in tissues, contraction of the human prostate to noradrenaline is therefore mediated by an alpha 1A-adrenoceptor.
Glycoprotein folding and the role of EDEM1, EDEM2 and EDEM3 in degradation of folding‐defective glycoproteins (2007)

Proteins synthesized in the endoplasmic reticulum (ER) lumen are exposed to several dedicated chaperones and folding factors that ensure efficient maturation. Nevertheless, protein folding remains error-prone and mutations in the polypeptide sequence may significantly reduce folding-efficiency. Folding-incompetent proteins carrying N-glycans are extracted from futile folding cycles in the calnexin chaperone system upon intervention of EDEM1, EDEM2 and EDEM3, three ER-stress-induced members of the glycosyl hydrolase 47 family. This review describes current knowledge about mechanisms regulating folding and disposal of glycoproteins.
Transgenic Durum Wheat by Microprojectile Bombardment of Isolated Scutella (1997)

A biolistic transformation method was developed, for the first time, for durum wheat (Triticum turgidum L., 2n = 4x = 28; AABB) cultivar Medora using isolated scutella as target cells, gus as a reporter gene, and bar (herbicide resistance gene) as a selectable marker. An average of 116 GUS foci per scutellum were observed 2 days after bombardment. After selection for herbicide resistance by adding 5 mg/l L-phosphinothrlcin (L-PPT) to the medium during regeneration and spot application of 120 mg/l L-PPT on the leaves of regenerated plants, we identified five resistant piants from a total of 245 scutella bombarded. All these plants were fertile. Of the 1048 T1 seeds germinated from five lines (dwt1, dwt2, dwt3, dwt4, and dwt5), a total of 104 T1 plants were recovered that showed resistance to the herbicide glufosinate when sprayed at a concentration of 120 mg/l L-PPT. Some of the herbicide-resistant T1 plants exhibited phosphinothricin acetyltransferase (PAT) enzyme activity, indicating the presence of the bar gene in the transgenics. The integration of gus and bar genes into the genomes of durum wheat was further confirmed by Southern anaiysls. Development of this transformation procedure with an agronomically superior durum cultivar will open up new avenues for the enhancement of the existing germpiasm through biotechnology.
A Shape Memory Acrylamide/DNA Hydrogel Exhibiting Switchable Dual pH‐Responsiveness (2015)

Shape memory acrylamide/DNA hydrogels include two different crosslinkers as stabilizing elements. The triggered dissociation of one of the crosslinking elements transforms the shaped hydrogel into an arbitrarily shaped (or shapeless) quasi‐liquid state. The remaining crosslinking element, present in the quasi‐liquid, provides an internal memory that restores the original shaped hydrogel upon the stimulus‐triggered regeneration of the second crosslinking element. Two pH‐sensitive shape memory hydrogels, forming Hoogsten‐type triplex DNA structures, are described. In one system, the shaped hydrogel is stabilized at pH = 7.0 by two different duplex crosslinkers, and the transition of the hydrogel into the shapeless quasi‐liquid proceeds at pH = 5.0 by separating one of the crosslinking units into a protonated cytosine–guanine–cytosine (C–G·C + ) triplex. The second shaped hydrogel is stabilized at pH = 7.0, by cooperative duplex and thymine–adenine–thymine triplex (T–A·T) bridges. At pH = 10.0, the triplex units separate, leading to the dissociation of the hydrogel into the quasi‐liquid state. The cyclic, pH‐stimulated transitions of the two systems between shaped hydrogels and shapeless states are demonstrated. Integrating the two hydrogels into a shaped “two‐arrowhead” hybrid structure allows the pH‐stimulated cyclic transitions of addressable domains of the hybrid between shaped and quasi‐liquid states.
In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans (2006)

Of the 4727 ORFs in the genome of L. interrogans, 226 genes were identified as vaccine candidates by bioinformatics, CGH and transcriptional analysis on the basis of the theory of reverse vaccinology. The proteins encoded by these genes might be useful as vaccine candidates as well as for diagnosis of leptospirosis.
Practical Privacy-Preserving MapReduce Based K-Means Clustering Over Large-Scale Dataset (2017)

Clustering techniques have been widely adopted in many real world data analysis applications, such as customer behavior analysis, targeted marketing, digital forensics, etc. With the explosion of data in today's big data era, a major trend to handle a clustering over large-scale datasets is outsourcing it to public cloud platforms. This is because cloud computing offers not only reliable services with performance guarantees, but also savings on in-house IT infrastructures. However, as datasets used for clustering may contain sensitive information, e.g., patient health information, commercial data, and behavioral data, etc, directly outsourcing them to public cloud servers inevitably raise privacy concerns. In this paper, we propose a practical privacy-preserving K-means clustering scheme that can be efficiently outsourced to cloud servers. Our scheme allows cloud servers to perform clustering directly over encrypted datasets, while achieving comparable computational complexity and accuracy compared with clusterings over unencrypted ones. We also investigate secure integration of MapReduce into our scheme, which makes our scheme extremely suitable for cloud computing environment. Thorough security analysis and numerical analysis carry out the performance of our scheme in terms of security and efficiency. Experimental evaluation over a 5 million objects dataset further validates the practical performance of our scheme.
Conceptual development of nurse-physician collaboration (1994)

The concept of nurse-physician collaboration has significance in today's changing health care environment. Two camps' views concerning nurse-physician collaboration are presented. Camp I supports nurse-physician collaboration using four indicators: (1) mutual power-control, (2) separate and combined practice spheres, (3) mutual concerns, and (4) common patient goals. Camp II takes a totally different approach and describes the structure that must be present before collaboration may exist. The literature supports the use of both camps' views in developing measures for the concept of collaboration. Once these aspects of collaboration can be accurately measured then recommendations can be made concerning changes needed in health care delivery systems to effect outcomes.
Dynamical Graph Models of Aircraft Electrical, Thermal, and Turbomachinery Components (2017)

The current trend of electrification in modern aircraft has driven a need to design and control onboard power systems that are capable of meeting strict performance requirements while maximizing overall system efficiency. Model-based control provides the opportunity to meet the increased demands on system performance, but the development of a suitable model can be a difficult and time-consuming task. Due to the strong coupling between systems, control-oriented models should capture the underlying physical behavior regardless of energy domain or time-scale. This paper seeks to simplify the process of identifying a suitable control-oriented model by defining a scalable and broadly applicable approach to generating graph-based models of thermal, electrical, and turbomachinery aircraft components and systems. Subsequently, the process of assembling component graphs into a dynamical system graph that integrates multiple energy domains is shown. A sample electrical and thermal management system is used to demonstrate the capability of a graph model at matching the complex dynamics exhibited by nonlinear and empirically based simulation models.
Characterization of <i>Listeria monocytogenes</i> Strains Involved in Invasive and Noninvasive Listeriosis Outbreaks by PCR-Based Fingerprinting Techniques (2001)

A total of 32 Listeria monocytogenes strains (16 from a recent outbreak of invasive listeriosis and 16 from two outbreaks of noninvasive listeriosis, all three occurring in Italy) were characterized by PCR-ribotyping, arbitrarily primed PCR (AP-PCR), and the recently developed infrequent-restriction-site PCR (IRS-PCR). The discriminatory ability of the techniques, first evaluated on 29 unrelated L. monocytogenes food isolates using Simpson's index of diversity, was 0.714 for PCR-ribotyping, 0.690 for AP-PCR, and 0.919 for IRS-PCR. IRS-PCR was also more capable of distinguishing among strains from the invasive listeriosis outbreak: three different clusters were identified by IRS-PCR compared to two clusters identified by both PCR-ribotyping and AP-PCR. Within each of the two outbreaks of noninvasive listeriosis, the patterns were practically identical, as demonstrated by all three techniques. Only IRS-PCR succeeded in clearly discriminating the strains related to noninvasive listeriosis from all of the other strains included in this study, including those from the outbreak of invasive listeriosis. This finding may suggest the presence of unique differences in their DNA sequences.
Necessity of re‐evaluation of estramustine phosphate sodium (EMP) as a treatment option for first‐line monotherapy in advanced prostate cancer (2001)

Estramustine phosphate sodium (EMP) was first introduced in the early 1970s for the treatment of prostate cancer, when EMP was supposed to have the dual effect of estrogenic activity and cytotoxicity. For the following decades, it was used mainly in hormone-refractory cases, with a conventional dosage of 4-9 capsules/day, which showed a 30-35% objective response rate. However, a very limited number of cases have been reported that used EMP as a first-line monotherapy in the conventional dosage. One study showed a response rate of 82%, which is at least as effective as conventional estrogen (diethylstilbestrol; DES) monotherapy. Nevertheless, EMP was almost abandoned for the treatment of prostate cancer because of severe adverse side-effects, especially in the cardiovascular system and gastrointestinal tract. Recently, two facts have become evident. First, EMP interferes with cellular microtubule dynamics but does not show alkylating effects. Second, EMP is able to produce a complex with calcium when dairy products are taken concomitantly with EMP, resulting in a decrease in the absorption rate of EMP from the gut. Many clinical trials have been undertaken without warning against concomitant dairy product intake since the introduction of EMP. This fact will jeopardize almost all the clinical trials performed before 1990. It is considered that response rates have been underestimated and better results could have been obtained because side-effects decrease dose-dependently. Low-dose EMP monotherapy (2 capsules/day) has been performed infrequently in previously untreated advanced prostate cancer. The only large trial by the European Organization for Research and Treatment of Cancer in 1984 was biased in selecting patients. Nevertheless, the response rate of EMP is comparable to that of DES. In this study, the adverse side-effects of EMP were less than that of DES. Recently, a study was conducted at the University of Tokyo of 11 patients with advanced prostate cancer on low-dose EMP as first-line monotherapy. The study found that the mean serum prostate-specific antigen level decreased to within the normal range by day 50; mean serum testosterone, leutinizing hormone and follicle-stimulating hormone reduced to undetectable levels by day 20; and mean serum estradiol increased to a very high level within 1 week. These data implicate that low-dose EMP can suppress quickly and adequately the pituitary-gonadal axis, although the antitumor effect has not as yet been elucidated. For these reasons, it is necessary to re-evaluate low-dose EMP monotherapy in previously untreated advanced prostate cancer.
MACHINE PERCEPTION OF VISUAL-MOTION (1985)

Recent work carried out, in England, on optical flow techniques in computer vision is described. The background, principles and implementation of the algorithms derived for machine perception and interpretation of visual motion are discussed in order to give an overall picture of developments to date. It is concluded that we have a first attempt at devising a system for using visual motion to obtain 3D scene information at the level of Marr's 2 one-half D sketch. The algorithms proposed can be implemented efficiently on an SIMD processor array and in the ideal case of a direct 1:1 mapping of the image pixels on to the processor array run at speeds approaching real-time video frame rates on existing machines. Some suggestions for future work are indicated.
사교육의 개념 및 전제에 대한 철학적 검토 (2018)

이 논문은 우리나라에 사교육 현상이 만연하여 문제시되고 있는 상황을 올바르게 탐구하고 있는지에 대한 문제의식에서 출발한다. 이를 위해 기존의 사교육 정책들이 가지고 있는 특징과 논리적 가정을 살펴본다. ‘공교육정상화를 위한 사교육 규제’라는 기치로 표현되는 사교육 정책들은 사교육을 억제해야 하는 부정적인 것이고, 공교육에 방해되는 것이라고 가정하고 있다. 그러나 이 두 전제가 토대를 두고 있는 사교육의 개념은 별도의 검토가 필요한 문제들이다.
기존의 사교육 개념은 ‘경제적 정의’, ‘제도적 정의’, ‘현상적 정의’로 나눌 수 있으며, 현재 우리나라 사교육의 주요 정책 및 연구는 현상적 정의에 기반을 두고 있다. 각각의 정의는 개념적으로 약점이 존재하며, 특히 현상적 정의는 (1)사교육을 부정적인 것으로 보고, (2)공교육과 사교육의 관계를 적대적으로 보며, (3)사교육의 양태들을 종합적으로 포착하지 못하는 문제점이 있다. 이러한 문제점들은 사교육의 연구 및 정책의 방향을 왜곡시키기 때문에 사교육 개념에 대한 대안적인 정의가 필요하다. 이 논문에서는 현상적 정의의 편견을 바로잡는 소극적 접근으로 ‘기능적 해석’을, 현상 이면의 특성을 탐구하는 적극적 접근으로 ‘교육열을 통한 해석’을 각각 검토하고, 두 접근에서 결여된 교육적 의미를 정립하기 위하여 ‘좋은 삶(the good life)’을 위한 교육적 접근을 제시한다.
Composition and Toxicity of the Inclusion of <i>Bacillus thuringiensis</i> subsp. <i>israelensis</i> (1985)

The multisegmented ovoidal inclusion of Bacillus thuringiensis subsp. israelensis was found to be composed of two structurally and biochemically distinct components. Electron microscopy of the inclusion revealed it to be composed mainly of osmiophobic or lightly stained segments crystallized in a lattice showing a repeat of approximately 4.3 nm. These light segments of the inclusions were shared by osmiophylic darkly stained segments with a crystal lattice repeat of approximately 7.8 nm. The lightly stained segments were soluble at pH 9.2 in sodium dodecyl sulfate-dithiothreitol-Tris-hydrochloride. The extracts of lightly stained segments were lytic to mammalian erythrocytes, and the precipitate obtained by lowering the pH to 5.2 was toxic to the larvae of Aedes egypti. The dark inclusion segments remaining, besides being much less toxic to larvae, were nonlytic to erythrocytes and were soluble at pH 10.5 in sodium dodecyl sulfate-dithiothreitol-Tris-hydrochloride. The light segment was composed of two major polypeptide doublets with molecular weights of 145,000 and 135,000, and 27,000 and 26,500, and the dark segments were composed of a single major polypeptide with a molecular-weight of 70,000. Hence, the inclusion of B. thuringiensis subsp. israelensis is more complex than previously reported, and we conclude that the toxin may be the polypeptide with a molecular weight of 27,000 and 26,500.
Geometry from a Differentiable Viewpoint (1995)

Differential geometry has developed in many directions since its beginnings with Euler and Gauss. This often poses a problem for undergraduates: which direction should be followed? What do these ideas have to do with geometry? This book is designed to make differential geometry an approachable subject for advanced undergraduates. The text serves as both an introduction to the classical differential geometry of curves and surfaces and as a history of the non-Euclidean plane. The book begins with the theorems of non-Euclidean geometry, then introduces the methods of differential geometry and develops them towards the goal of constructing models of the hyperbolic plane. Interesting diversions are offered, such as Huygens' pendulum clock and mathematical cartography; however, the focus of the book is on the models of non-Euclidean geometry and the modern ideas of abstract surfaces and manifolds. Although the main use of this text is as an advanced undergraduate course book, the historical aspect of the text should appeal to most mathematicians.
Real Time Engine Control Using STR in Feedback System (1995)

<div class="htmlview paragraph">This research project involved work into the application of a Self Tuning Regulator (STR), one type of adaptive control technique used in the real-time control of internal combustion engines in order to enhance the air/fuel controllability. We concentrated on the target air/fuel and output air/fuel values, and applied adaptive control to the feedback system. With this structure, equivalence transformation of a conventional PID feedback controller to STR can be performed. Through simulation, it was confirmed the effectiveness of the controllability and disturbance robustness, and controllability verification tests were performed using real-time engine control on an actual vehicle in the FTP75 LA-4 mode. This resulted in a dramatic improvement in air/fuel controllability.</div>
Analysis of differentially expressed genes in<i>Oryza meyeriana</i>in response to infection by<i>Xanthomonas oryzae</i>pv.<i>oryzae</i> (2009)

With 2 tables and 6 figures Abstract Oryza meyeriana Baill was found immune to Xanthomonas oryzae pv. oryzae (Xoo). However, the genes responsible for the strong resistance are unknown. In this study, suppression subtractive hybridization (SSH) was utilized to identify genes differentially expressed in O. meyeriana after Xoo infection. Oryza meyeriana plants inoculated with high pathogenicity races were used as ‘tester’ and non-inoculated plants as ‘driver’. Analysis of the SSH library revealed genes responsible for cell wall lignifications, which may function to block pathogen invasion. Also identified are genes involved in secondary metabolism systems to eliminate damage caused by chemicals such as peroxides in cells. One of the response genes, ME281 encoding a protein with leucine-rich repeats which has high similarity with those of other reported disease resistance genes, was further analysed by RT-PCR and Northern blotting, which showed its expression peaked at 48–72 h after Xoo infection, suggesting that it may function at the later stage of the plant’s responses. This study would help demonstrate the molecular mechanism of O. meyeriana’s strong resistance to Xoo and find new disease resistance candidate genes.
Studies of the N-Terminal Region of a Parathyroid Hormone-Related Peptide(1-36) Analog: Receptor Subtype-Selective Agonists, Antagonists, and Photochemical Cross-Linking Agents (1999)

The N-terminal regions of PTH and PTH-related peptide (PTHrP) are involved in receptor-mediated signaling and subtype selectivity. To better understand the molecular basis for these processes, we first prepared a series of[ I5,W23,Y36]-PTHrP(1–36)NH2 analogs having stepwise deletions of residues 1–4 and characterized them with the human (h)PTH-1 and hPTH-2 receptor subtypes stably transfected in LLC-PK1 cells. Deletions beyond residue 2 caused progressive and severe losses in cAMP-signaling efficacy without dramatically diminishing receptor-binding affinity; consistent with this, [I5,W23]-PTHrP(5–36) was a potent antagonist for both PTH receptor subtypes. We then prepared and characterized photolabile analogs of[ I5,W23,Y36]-PTHrP(1–36)NH2 that were singly modified with para-benzoyl-l-phenylalanine (Bpa) along the first six residues. These full-length analogs exhibited receptor subtype-selective agonism, antagonism, and photochemical cross-linking profiles. In particular, the [Bpa2]- and[ Bpa4]-substituted analogs selectively antagonized and preferentially cross-linked to the PTH-1 receptor and PTH-2 receptor, respectively. These results demonstrate that the 1–5 region of[ I5,W23]-PTHrP(1–36) is critical for activating the PTH-1 and PTH-2 receptors and suggest that the individual residues in this region play distinct roles in modulating the activation states of the two receptors. The cross-linking of both agonist and antagonist ligands to these PTH receptors lays the groundwork for identifying critical signaling determinants in the ligand binding pocket of the receptor.