gebhart/patrepeval huggingface dataset:
A Preliminary Analysis of the Immunoglobulin Genes in the African Elephant (Loxodonta africana) (2011)

The genomic organization of the IgH (Immunoglobulin heavy chain), Igκ (Immunoglobulin kappa chain), and Igλ (Immunoglobulin lambda chain) loci in the African elephant (Loxodonta africana) was annotated using available genome data. The elephant IgH locus on scaffold 57 spans over 2,974 kb, and consists of at least 112 V(H) gene segments, 87 D(H) gene segments (the largest number in mammals examined so far), six J(H) gene segments, a single μ, a δ remnant, and eight γ genes (α and ε genes are missing, most likely due to sequence gaps). The Igκ locus, found on three scaffolds (202, 50 and 86), contains a total of 153 V(κ) gene segments, three J(κ) segments, and a single C(κ) gene. Two different transcriptional orientations were determined for these V(κ) gene segments. In contrast, the Igλ locus on scaffold 68 includes 15 V(λ) gene segments, all with the same transcriptional polarity as the downstream J(λ)-C(λ) cluster. These data suggest that the elephant immunoglobulin gene repertoire is highly diverse and complex. Our results provide insights into the immunoglobulin genes in a placental mammal that is evolutionarily distant from humans, mice, and domestic animals.
Desmosomes: Regulators of Cellular Signaling and Adhesion in Epidermal Health and Disease (2014)

Desmosomes are intercellular junctions that mediate cell-cell adhesion and anchor the intermediate filament network to the plasma membrane, providing mechanical resilience to tissues such as the epidermis and heart. In addition to their critical roles in adhesion, desmosomal proteins are emerging as mediators of cell signaling important for proper cell and tissue functions. In this review we highlight what is known about desmosomal proteins regulating adhesion and signaling in healthy skin-in morphogenesis, differentiation and homeostasis, wound healing, and protection against environmental damage. We also discuss how human diseases that target desmosome molecules directly or interfere indirectly with these mechanical and signaling functions to contribute to pathogenesis.
Ultra-low crosstalk, CMOS compatible waveguide crossings for densely integrated photonic interconnection networks (2013)

We explore the design space for optimizing CMOS compatible waveguide crossings on a silicon photonics platform. This paper presents simulated and experimental excess loss and crosstalk suppression data for vertically integrated silicon nitride over silicon-on-insulator waveguide crossings. Experimental results show crosstalk suppression exceeding -49/-44 dB with simulation results as low as -65/-60 dB for the TE/TM mode in a waveguide crossing with a 410 nm vertical gap.
High-quality silicon on silicon nitride integrated optical platform with an octave-spanning adiabatic interlayer coupler (2015)

Hybrid nanophotonic platforms based on three-dimensional integration of different photonic materials are emerging as promising ecosystems for the optoelectronic device fabrication. In order to benefit from key features of both silicon (Si) and silicon nitride (SiN) on a single chip, we have developed a wafer-scale hybrid photonic platform based on the integration of a thin crystalline Si layer on top of a thin SiN layer with an ultra-thin oxide buffer layer. A complete optical path in the hybrid platform is demonstrated by coupling light back and forth between nanophotonic devices in Si and SiN layers. Using an adiabatic tapered coupling method, a record-low interlayer coupling-loss of 0.02 dB is achieved at 1550 nm telecommunication wavelength window. We also demonstrate high-Q resonators on the hybrid material platform with intrinsic Q's as high as 3 × 10(6) for a 60 μm-radius microring resonator, which is (to the best of our knowledge) the highest Q observed for a micro-resonator on a hybrid Si/SiN platform.
LFA-1 in T Cell Migration and Differentiation (2018)

Maintenance of homeostatic immune surveillance and development of effective adaptive immune responses require precise regulation of spatial and temporal lymphocyte trafficking throughout the body to ensure pathogen clearance and memory generation. Dysregulation of lymphocyte activation and migration can lead to impaired adaptive immunity, recurrent infections, and an array of autoimmune diseases and chronic inflammation. Central to the recruitment of T cells, integrins are cell surface receptors that regulate adhesion, signal transduction, and migration. With 24 integrin pairs having been discovered to date, integrins are defined not only by the composition of the heterodimeric pair but by cell-type specific expression and their ligands. Furthermore, integrins not only facilitate adhesion but also induce intracellular signaling and have recently been uncovered as mechanosensors providing additional complexity to the signaling pathways. Among several leukocyte-specific integrins, lymphocyte function-associated antigen-1 (LFA-1 or α<sub>L</sub>β<sub>2</sub>; CD11a/CD18) is a key T cell integrin, which plays a major role in regulating T cell activation and migration. Adhesion to LFA-1's ligand, intracellular adhesion receptor 1 (ICAM-1) facilitates firm endothelium adhesion, prolonged contact with antigen-presenting cells, and binding to target cells for killing. While the downstream signaling pathways utilized by LFA-1 are vastly conserved they allow for highly disparate responses. Here, we summarize the roles of LFA-1 and ongoing studies to better understand its functions and regulation.
ENPP2 Contributes to Adipose Tissue Expansion and Insulin Resistance in Diet-Induced Obesity (2014)

Body weight is tightly regulated by food intake and energy dissipation, and obesity is related to decreased energy expenditure (EE). Herein, we show that nucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2, autotaxin) is an adipose-derived, secreted enzyme that controls adipose expansion, brown adipose tissue (BAT) function, and EE. In mice, Enpp2 was highly expressed in visceral white adipose tissue and BAT and is downregulated in hypertrophied adipocytes/adipose tissue. Enpp2(+/-) mice and adipocyte-specific Enpp2 knockout mice fed a high-fat diet showed smaller body weight gains and less insulin resistance than control mice fed the same diet. BAT was functionally more active and EE was increased in Enpp2-deficient mice. In humans, ENPP2 expression in subcutaneous fat and ENPP2 levels in serum were reduced in obese subjects. Taken together, our results establish ENPP2 as an adipose-derived, secreted enzyme that regulates adipose obesity and systemic metabolism. They also suggest ENPP2 could be a useful therapeutic target for the treatment of metabolic disease.
Molecules That Mimic Apolipoprotein A-I: Potential Agents for Treating Atherosclerosis (2013)

Certain amphipathic α-helical peptides can functionally mimic many of the properties of full-length apolipoproteins, thereby offering an approach to modulate high-density lipoprotein (HDL) for combating atherosclerosis. In this Perspective, we summarize the key findings and advances over the past 25 years in the development of peptides that mimic apolipoproteins, especially apolipoprotein A-I (apoA-I). This assemblage of information provides a reasonably clear picture of the state of the art in the apolipoprotein mimetic field, an appreciation of the potential for such agents in pharmacotherapy, and a sense of the opportunities for optimizing the functional properties of HDL.
A role for Z-DNA binding in vaccinia virus pathogenesis (2003)

The N-terminal domain of the E3L protein of vaccinia virus has sequence similarity to a family of Z-DNA binding proteins of defined three-dimensional structure and it is necessary for pathogenicity in mice. When other Z-DNA-binding domains are substituted for the similar E3L domain, the virus retains its lethality after intracranial inoculation. Mutations decreasing Z-DNA binding in the chimera correlate with decreases in viral pathogenicity, as do analogous mutations in wild-type E3L. A chimeric virus incorporating a related protein that does not bind Z-DNA is not pathogenic, but a mutation that creates Z-DNA binding makes a lethal virus. The ability to bind the Z conformation is thus essential to E3L activity. This finding may allow the design of a class of antiviral agents, including agents against variola (smallpox), which has an almost identical E3L.
Optimization of cooperative spectrum sensing with energy detection in cognitive radio networks (2009)

We consider cooperative spectrum sensing in which multiple cognitive radios collaboratively detect the spectrum holes through energy detection and investigate the optimality of cooperative spectrum sensing with an aim to optimize the detection performance in an efficient and implementable way. We derive the optimal voting rule for any detector applied to cooperative spectrum sensing. We also optimize the detection threshold when energy detection is employed. Finally, we propose a fast spectrum sensing algorithm for a large network which requires fewer than the total number of cognitive radios in cooperative spectrum sensing while satisfying a given error bound.
SOCIAL STRATIFICATION AND PARENT—CHILD RELATIONS IN WASHINGTON, DC (2019)

My wife and I were now in Washington. We had a warm welcome from my new associates, mainly young sociologists – Manny Rosenberg, Len Pearlin, Erving Goffman, and others soon to arrive. I knew what I wanted to do: A study of social stratification and family relationships. I was not thrilled at the idea of doing such a study in Washington, DC, because Washington was so atypical a city. But I had little choice in the matter, and Washington was not a bad place to begin such research. Our budget was limited. Basically, I could hire a few young people as my staff, and that was it. It was enough. The young people were wonderful – enthusiastic, quick to learn, and cooperative. Numerous studies of social stratification and parent–child relationships appeared before ours, mainly by psychologists, all of them focused on particular parental practices – bottle-feeding or breastfeeding, and the frequency of using particular disciplinary practices when their children misbehaved. I had tried my damnedest to make sense of this literature and had given up in despair. My former teacher and close friend, Urie Bronfenbrenner, outdid me, though, and made eminently sensible descriptive sense of the entire body of literature. He arrayed the studies, not in sequence of their dates of publication, but of their dates of fieldwork , and discovered that there had been great changes over time in the practices that parents followed , from restrictive to permissive. Middle-class parents had led the way, always about several years ahead of working-class parents. I questioned Urie regarding his further interpretation, that the reason middle-class parents led the way was because of their greater education. I suggested, instead, that while their greater education led middleclass parents to be more likely to read the experts’ books, as we knew they did, they need not have followed the experts. That they did follow the experts was not , to my thinking, because they blindly followed expert advice, but because the experts gave them useful advice, consistent with their values. What I did instead was to approach the entire issue from a vastly different perspective, the perspective of sociological theory.
논문 : 도시 환경색채 개선에 관한 연구 - 서울특별시 용산구 이촌 1 동을 중심으로 - (2001)

도시경관과 도시환경은 도시를 구성하는 자연과 건축물을 포함한 인공 구조물 등의 형태와 색채에 의해 결정되어진다 형태는 색채보다 우위에 있지만 형태를 결정하는 요인은 경제적 공학적, 사회적 문제 등을 고려해야 하기 때문에 매우 복잡하고 관리가 어렵다. 그러므로 도시환경개선을 위해서는 형태에 앞서 색채요소를 검토하는 것이 관리 개선 차원에서 경제적 효율성이 크다고 할 수 있다. 심리적 , 생리적, 물리적 성질을 이용하여 적절하게 계획된 환경색채의 사용은 바람직한 도시경관을 만들어준다. 본 연구에서 조사된 이촌1동의 환경색채현황은 각기 다른 이름을 가진 아파트에 각기 다른 색채를 사용함으로서 색채가 범람하여 시각적으로 혼란스러움을 야기 시킨다. 이를 개선하기 위해서는 소단지의 아파트군으로 형성된 지역적 특징을 고려하여 그룹핑(grouping)해서 색채계획을 블록 혹은 구덕별로 나누어서 하는 것이 요구된다 사용색채는 주조색과 보조색 혹은 강조색을 적용한다. 주조색(face color)은 우변의 자연 환경색과 조화로운 색채를 부여하여야 한다. 주조색의 단계적 색조 변화로 그룹핑 한곳을 구분할 경우 식별도 용이하고 변화와 통일감을 줄수 있다 적절한 보조색의 사용은 사람들에게 활기와 생명력을 불러일으킨다 수퍼그래픽, 아파트의 이름, 동표시 등도 유기적 관계 속에서 전체적인 이미지에 부합되게 색채, 형태, 크기 등이 디자인되어야 한다.
결과적으로 환경색채는 분명한 목적과 계획아래 이루어졌을 때 쾌적하고 아름다운 환경을 제공할 수 있다.
Interpretation of partial discharges at dc voltages (1995)

The aim of this paper is to give an overview on partial discharges at dc voltage. A model is presented which describes the stochastic discharge process. The model is experimentally verified for internal discharges and for corona in air. In addition, the classification of discharge patterns is discussed. The 3-dimensional histogram describing the number of discharges depending on the discharge magnitude and on the time to the successive discharge is suggested to be used as a base for discharge recognition at dc voltage. Experimental proof is presented to show the strength of this approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cerebral palsy: A rational approach to a treatment protocol, and the role of botulinum toxin in treatment (1997)

Cerebral palsy (CP) is characterized by aberrant control of movement or posture and appears early in life secondary to central nervous system damage. The symptoms of CP fall into four groups: symptoms due to loss of selective motor control; symptoms due to abnormal muscle tone; symptoms due to imbalance between muscle agonists and antagonists; and symptoms due to impaired balance. The goals of treatment are to maximize function and minimize the development of joint contracture and other secondary problems. Development of a treatment plan begins with the definition of objectives and consideration of the effects of growth and development on the patient's abilities. The role of botulinum toxin in CP treatment has grown in recent years. The patient who could benefit most from botulinum toxin treatment is one who is hypertonic and whose abnormal muscle tone is interfering with function, or who is expected to develop joint contracture with growth because of this abnormal tone. By altering this muscle tone, function can be enhanced or additional therapeutic modalities can be employed. Assessing treatment outcomes for BTX injection involves the same set of questions and measurements as for other types of treatments and depends on the careful definition of treatment objectives beforehand.
Network Security Risk Assessment Based on Attack Graph (2013)

In order to protect the network and evaluate the network security risks automatically, a new multi-agents risk assessment model based on attack graph (MRAMBAG) is presented. First, a network risk assessment model with master-slave agents is established, especially the functional architecture of master-slave agents and the risk association relation analysis process are designed. Then, the attack path and the attack graph are constructed by using the Attract Graph Building algorithm with the input of the dynamic data information collected by components. Finally, risk indexes of attack path, components, hosts, vulnerabilities and association risk index of network nodes are calculated successively and consequently the security risk quantitative index of target networks are obtained. The experimental results demonstrate that the MRAMBAG is a more feasible and effective way for evaluate the network security risk.
Homologs of the essential ubiquitin conjugating enzymes UBC1, 4, and 5 in yeast are encoded by a multigene family in Arabidopsis thaliana (1993)

The covalent attachment of the 76 amino acid protein ubiquitin is an important prerequisite for the degradation of many eukaryotic proteins. The specificity of this ligation is accomplished in part by a family of distinct ubiquitin conjugating enzymes (E2s) working in concert with specific ubiquitin-protein ligases (E3s). Three essential E2s in yeast encoded by ScUBC1, -4, and -5 comprise a functionally overlapping E2 subfamily that appears responsible for degrading most abnormal and short-lived proteins. A 15 kDa E2 protein homologous to this family has been identified previously in wheat germ, designated TaE2(15kDa) (Girod and Vierstra (1993) J. Biol. Chem. 268, 955-960). This E2 is responsible for much of the ubiquitin conjugating activity observed in wheat germ extracts and works together with a unique E3 (designated E3 gamma) for substrate recognition. In this paper, the cloning of five genes encoding E2(15kDa) from Arabidiopsis thaliana is described (designated AtUBC8-12). They encode 149 amino acid basic proteins 94-98% similar to each other and 88-92% similar to ScUBC4 at the amino acid sequence level. In contrast, AtUBC8-12 are only 55-65% similar to the Arabidopsis E2s encoded by AtUBC1, -4, and -7. The AtUBC8-12 proteins do not contain N- or C-terminal extensions and have the active site at residue Cys-86, based on their homology with other E2s. Analyses of genomic Southern blots are consistent with the existence of multiple members encoding this E2 subfamily. AtUBC8-12 are transcribed to yield about 800 nucleotide mRNAs that, unlike ScUBC4 and -5, are not strongly induced by heat shock.(ABSTRACT TRUNCATED AT 250 WORDS)
Mechanism for Flow-Rate Controlled Breakup in Confined Geometries: A Route to Monodisperse Emulsions (2005)

This Letter describes a quasistationary breakup of an immiscible, inviscid fluid at low capillary numbers. The breakup proceeds in a coflowing, viscous liquid, in a confined geometry of a long and narrow orifice. In contrast to the capillary instability in an unbounded fluid, the collapse proceeds through a series of equilibria, each yielding the minimum interfacial energy of the fluid-fluid interface. The process is slow in comparison to typical relaxation speeds of the interface, and it is reversible. Its quasistatic character of collapse forms the basis for controlled, high-throughput generation of monodisperse fluid dispersions.
Installation Effects of a Propeller Mounted on a High-Lift Wing with a Coanda Flap. Part I: Aeroacoustic Experiments (2014)

In this contribution, we present aeroacoustic experiments concerning installation effects of propellers. Such installation effects are important as they can significantly alter the sound radiation as compared to an isolated propeller. For this purpose, detailed experiments have been conducted in the NWB aeroacoustic wind tunnel in Braunschweig, Germany. The considered geometry is a nine-bladed propeller installed in front of a high-lift wing (employing a Coanda flap). The results illustrate the influence of propeller rotational speed, blade pitch angle, wind tunnel velocity, and angle of attack variations on the sound radiation. Furthermore, with a source localisation technique insight is gained in the dominant sound sources, and reveals the importance of periodic as well as broadband noise for the considered geometry.
One pot ‘click’ reactions: tandem enantioselective biocatalytic epoxide ring opening and [3+2] azide alkyne cycloaddition (2010)

Halohydrin dehalogenase (HheC) can perform enantioselective azidolysis of aromatic epoxides to 1,2-azido alcohols which are subsequently ligated to alkynes producing chiral hydroxy triazoles in a one-pot procedure with excellent enantiomeric excess.
Ovarian cancer side population defines cells with stem cell-like characteristics and Mullerian Inhibiting Substance responsiveness (2006)

The recent identification of "side population" (SP) cells in a number of unrelated human cancers and their normal tissue sources has renewed interest in the hypothesis that cancers may arise from somatic stem/progenitor cells. The high incidence of recurrence attributable to multidrug resistance and the multiple histologic phenotypes indicative of multipotency suggests a stem cell-like etiology of ovarian cancer. Here we identify and characterize SP cells from two distinct genetically engineered mouse ovarian cancer cell lines. Differential efflux of the DNA-binding dye Hoechst 33342 from these cell lines defined a human breast cancer-resistance protein 1-expressing, verapamil-sensitive SP of candidate cancer stem cells. In vivo, mouse SP cells formed measurable tumors sooner than non-SP (NSP) cells when equal numbers were injected into the dorsal fat pad of nude mice. The presence of Mullerian Inhibiting Substance (MIS) signaling pathway transduction molecules in both SP and NSP mouse cells led us to investigate the efficacy of MIS against these populations in comparison with traditional chemotherapies. MIS inhibited the proliferation of both SP and NSP cells, whereas the lipophilic chemotherapeutic agent doxorubicin more significantly inhibited the NSP cells. Finally, we identified breast cancer-resistance protein 1-expressing verapamil-sensitive SPs in three of four human ovarian cancer cell lines and four of six patient primary ascites cells. In the future, individualized therapy must incorporate analysis of the stem cell-like subpopulation of ovarian cancer cells when designing therapeutic strategies for ovarian cancer patients.
Mutation of twins encoding a regulator of protein phosphatase 2A leads to pattern duplication in Drosophila imaginal discs. (1993)

The Drosophila gene twins was identified through a P-element-induced mutation that caused overgrowth in posterior regions of the wing imaginal disc. Analyses using position-specific markers showed that the inactivation of this locus induced the formation of extra wing blade anlagen in the posterior compartment of the disc. The duplication was mirror symmetrical, and the line of the symmetry did not correspond to any of the known compartment borders. We isolated the twins gene and found that it encoded one of the regulatory subunits of protein phosphatase 2A (PP2A). These results suggest a novel aspect of physiological roles of protein dephosphorylation; that is, the control of PP2A activity is crucial for specification of tissue patterns.
Morphine Induces Late Cardioprotection in Rat Hearts In Vivo: The Involvement of Opioid Receptors and Nuclear Transcription Factor ??B (2005)

Like lipopolysaccharide, morphine induces late preconditioning and activation of nuclear transcription factor-kappaB. Opioid receptors are involved as mediators in both morphine- and lipopolysaccharide-induced late preconditioning but as triggers only in morphine-induced late preconditioning.
Free-Solution, Label-Free Molecular Interactions Studied by Back-Scattering Interferometry (2007)

Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.
Introducing Multilevel Modeling (1998)

Introduction Overview of Contextual Models Varying and Random Coefficient Models Analyses Frequently Asked Questions