gebhart/patrepeval huggingface dataset:
Defect criticality index (DCI): a new methodology to significantly improve DOI sampling rate in a 45nm production environment (2008)

Increasing inspection sensitivity may be necessary for capturing the smaller defects of interest (DOI) dictated by reduced minimum design features. Unfortunately, higher inspection sensitivity can result in a greater percentage of non-DOI or nuisance defect types during inline monitoring in a mass production environment. Due to the time and effort required, review sampling is usually limited to 50 to 100 defects per wafer. Determining how to select and identify critical defect types under very low sampling rate conditions, so that more yield-relevant defect Paretos can be created after SEM review, has become very important. By associating GDS clip (design layout) information with every defect, and including defect attributes such as size and brightness, a new methodology called Defect Criticality Index (DCI) has demonstrated improved DOI sampling rates.
Selective enhancement of emotional, but not motor, learning in monoamine oxidase A-deficient mice (1997)

Mice deficient in monoamine oxidase A (MAOA), an enzyme that metabolizes monoamines such as norepinephrine and serotonin, have elevated norepinephrine and serotonin levels in the frontal cortex, hippocampus, and cerebellum, compared with normal wild-type mice. Since monoamines in these areas are critically involved in a variety of behaviors, we examined learning and memory (using emotional and motor tasks) in MAOA mutant mice. The MAOA-deficient mice exhibited significantly enhanced classical fear conditioning (freezing to both tone and contextual stimuli) and step-down inhibitory avoidance learning. In contrast, eyeblink conditioning was normal in these mutant mice. The female MAOA-deficient mice also displayed normal species-typical maternal behaviors (nesting, nursing, and pup retrieval). These results suggest that chronic elevations of monoamines, due to a deletion of the gene encoding MAOA, lead to selective alterations in emotional behavior.
Representation Learning for Information Extraction from Form-like Documents (2020)

We propose a novel approach using representation learning for tackling the problem of extracting structured information from form-like document images. We propose an extraction system that uses knowledge of the types of the target fields to generate extraction candidates, and a neural network architecture that learns a dense representation of each candidate based on neighboring words in the document. These learned representations are not only useful in solving the extraction task for unseen document templates from two different domains, but are also interpretable, as we show using loss cases.
Methylation-controlled J-protein MCJ acts in the import of proteins into human mitochondria (2012)

Loss of expression of the methylation-controlled J gene, MCJ (DNAJC15), is observed in cases of several tumors and plays a crucial role in the chemoresistance of ovarian cancer cells. Aside from the pathophysiological effects, almost nothing is known about the cellular function of MCJ. Here, we provide the first evidence that MCJ acts in the biogenesis of mitochondria. Our results demonstrate that MCJ is located in mitochondria. It is anchored in the mitochondrial inner membrane with the C-terminal J domain facing the matrix space. We show that MCJ forms a stable subcomplex with a component of the mitochondrial import motor, MAGMAS, a protein overexpressed in cells treated with granulocyte-macrophage colony-stimulating factor and in prostate carcinomas. In addition, MCJ and MAGMAS interact with the core components of the TIM23 pre-protein translocase. We demonstrate that the recombinant soluble MCJ domain stimulates the ATPase activity of the human mtHsp70 chaperone, mortalin, the central component of the import motor of the TIM23 translocase. This stimulation is counteracted by MAGMAS. Moreover, pre-protein import into mitochondria is impaired in the absence of MCJ. Interestingly, MCJ is able to take over the function of Tim14, the essential J co-chaperone of the mitochondrial protein import motor in yeast. In summary, our results show that MCJ functions as J co-chaperone of the human TIM23 pre-protein translocase, suggesting a link between mitochondrial pre-protein import and tumorigenesis.
Trends in Microfluidics with Complex Fluids (2003)

The rapid developments in biotechnology create a great demand for fluid handling systems on the nano- and picoliter scale. The characterization of minute quantities of DNA or protein samples requires highly integrated, automated, and miniaturized "total analysis systems" (mu-TAS). The small scales necessitate new concepts for devices both from a technological and from a fundamental physical point of view. Here, we describe recent trends in both areas. New technologies include soft lithography, chemical, and topographical structuring of surfaces in order to define pathways for liquids, as well as electro-wetting for manipulation purposes. Fundamentally, the interplay between geometric confinement and the size of biological macromolecules gives rise to complex dynamic behavior. The combination of both fluorescence imaging and scattering techniques allows for detailed insight into the dynamics of individual molecules and into their self-assembly into supramolecular aggregates.
Reversibility of chemotherapy-induced senescence is independent of autophagy and a potential model for tumor dormancy and cancer recurrence (2017)

Abstract Autophagy and senescence are both well-established responses to chemotherapy and radiation that often occur in parallel, contributing to growth arrest in tumor cells. However, it has not been established whether this growth arrest is reversible. This question was addressed using non-small cell lung cancer models exposed to the cancer chemotherapeutic drug, etoposide. Senescent cells that were sorted, identified by β-galactosidase staining and alterations in morphology, isolated by flow cytometric cell sorting based on C 12 FDG staining, and real-time live microscopy were found to be capable of recovering proliferative capacity. Autophagy, monitored by vacuole formation, SQSTM1/p62 degradation, and LC3BII generation did not interfere with either the senescence arrest or proliferative recovery and was nonprotective in function (i.e. autophagy inhibition via both pharmacological and genetic strategies had negligible impact on the response to etoposide). These observations argue against the premise that (chemotherapy-induced) senescence is irreversible and indicate that therapy-induced senescence may ultimately be a transient process in that at least a subpopulation of tumor cells can and will remain metabolically active and recover proliferative capacity independently of autophagic turnover. We therefore propose that dormant tumor cells may be capable of prolonged survival in a state of autophagy/senescence and that disease recurrence may reflect escape from this senescence-arrested state.
3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures (2015)

A 3D printable and highly stretchable tough hydrogel is developed by combining poly(ethylene glycol) and sodium alginate, which synergize to form a hydrogel tougher than natural cartilage. Encapsulated cells maintain high viability over a 7 d culture period and are highly deformed together with the hydrogel. By adding biocompatible nanoclay, the tough hydrogel is 3D printed in various shapes without requiring support material.
Mielopatia associada ao vírus linfotrópico humanode células T do tipo 1 (HTLV-1) (2002)

HTLV-1-associated myelopathy (HAM), also known as tropical spastic paraparesis (TSP), is a chronic progressive demyelinating disease that affects the spinal cord and white matter of the central nervous system. The lifetime incidence of HAM in HTLV-1 carriers is estimated to be less than 5%. Typical time of onset is in the fourth decade of life, with a female-to-male rate of 2:1. Gait disturbance and weakness and stiffness of the lower limbs are common presenting signs and symptoms of HAM. Lower extremities are affected to a much greater degree than upper extremities. Spasticity may be moderate to severe, and lower back pain is common. As the disease progresses, bladder and bowel dysfunction can occur. Sensory involvement is generally mild and can result in a variable degree of sensory loss and dysesthesia. Results of magnetic resonance imaging may be normal, or the scans show atrophy of the spinal cord and nonspecific lesions in the brain. Immunologic evidence suggests that an immune mechanism may play a role in the development of HAM. There is no effective treatment for the myelopathy. Corticosteroids, and INF-gamma may produce transient responses. Danazol, an anabolic steroid, does not improve gait and bladder function. The value of zidovudine (anti-retroviral agent) in the treatment has not been defined yet.
Multiple genetic alterations in human carcinogenesis. (1992)

Cancer development in man appeared to be a multistage process as suggested by epidemiological studies on commonly occurring gastric, colon, and breast cancers and also on human retrovirus-related leukemia, and by the finding by physicians and surgeons of precancerous lesions for many types of neoplasias. In the last 10 years it has become evident that human cancers have multiple genetic alterations caused by point mutations, recombinations, amplifications, and/or deletions. The genes affected include both oncogenes and tumor-suppressor genes and genes that accelerate cell proliferation and metastasis. Cancers with more malignant properties and poorer prognosis are generally associated with larger numbers of genetic alterations. These multiple genetic alterations are considered to be a direct reflection of the multiple steps involved in carcinogenesis. The multiple genetic alterations are caused by multiple environmental carcinogenic substances or factors, each of which usually exists only at minute concentrations and does not exert any major impact alone except under particular occupational, iatrogenic, and locally geographic conditions. The fact that carcinogenesis is a multistep process involving multiple genetic alterations clearly needs to be taken into consideration in assessing the risks of environmental carcinogenic substances or factors. The increasing incidence of multiple primary cancers is also most easily understood from the viewpoint of multiple steps in carcinogenesis. Possible multiple approaches to cancer prevention should therefore be considered in relation to multistep carcinogenesis and multiple carcinogenic factors.
Transcriptional Pathway Signatures Predict MEK Addiction and Response to Selumetinib (AZD6244) (2010)

Selumetinib (AZD6244, ARRY-142886) is a selective, non-ATP-competitive inhibitor of mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK)-1/2. The range of antitumor activity seen preclinically and in patients highlights the importance of identifying determinants of response to this drug. In large tumor cell panels of diverse lineage, we show that MEK inhibitor response does not have an absolute correlation with mutational or phospho-protein markers of BRAF/MEK, RAS, or phosphoinositide 3-kinase (PI3K) activity. We aimed to enhance predictivity by measuring pathway output through coregulated gene networks displaying differential mRNA expression exclusive to resistant cell subsets and correlated to mutational or dynamic pathway activity. We discovered an 18-gene signature enabling measurement of MEK functional output independent of tumor genotype. Where the MEK pathway is activated but the cells remain resistant to selumetinib, we identified a 13-gene signature that implicates the existence of compensatory signaling from RAS effectors other than PI3K. The ability of these signatures to stratify samples according to functional activation of MEK and/or selumetinib sensitivity was shown in multiple independent melanoma, colon, breast, and lung tumor cell lines and in xenograft models. Furthermore, we were able to measure these signatures in fixed archival melanoma tumor samples using a single RT-qPCR-based test and found intergene correlations and associations with genetic markers of pathway activity to be preserved. These signatures offer useful tools for the study of MEK biology and clinical application of MEK inhibitors, and the novel approaches taken may benefit other targeted therapies.
Environment Influences Functional Outcome of Cerebral Infarction in Rats (1995)

The laboratory environment is important for the functional outcome in brain ischemia. We hypothesize that an enriched environment may stimulate mechanisms that enhance brain plasticity after focal brain ischemia.
Internet broadcasting (1982)

Broadcasting should be a standard addressing mode of all packet-switched computer networks. Further, when networks are interconnected to form an internet, a broadcast mechanism is also required.
Broadcasting is the delivery of a packet to all hosts in a network; unicasting is the delivery of a packet to one specific host. They are distinct forms of interprocess communication; functions that are simple to do with one are difficult to do using only the other.
A broadcast is used when you don't know whom specifically to address. There are two situations where this occurs: (1) when you are searching for some information but you don't know who to ask (for example, standing up in a theatre and saying Is there a doctor in the house?), and (2) when you possess some information of use to others but you don't know specifically who (for example, standing up in a theatre and yelling Fire!).
A network should give its best efforts to deliver a copy of a broadcast packet to each host, but perfectly reliable delivery is not required. It is sufficient that most hosts receive a broadcast and that the same hosts not miss retransmissions. Just as with unicasting, higher-level protocols can be used to improve the reliability of the basic broadcast delivery mechanism, if required. Such an unreliable broadcast mechanism is straightforward to implement in all types of packet-switched networks.
In an internet composed of possibly thousands of networks and millions of hosts, a full internet-wide broadcast, the obvious internet analog to broadcasting in a single network, is seldom the right choice. A directed broadcast, delivery of a packet to all hosts on any single network in an internet, is simpler to implement, closer to what most users need, and sufficient to construct many forms of broadcast-based interprocess communication, including an internet-wide broadcast.
Biomass, growth rate, and production of filamentous fungi in plant litter (2002)

Heterotrophic organisms acquire their carbon and nutrients by one of two processes. Animals and protists are capable of ingesting particles, a mode of nutrition known as phagotrophy. Organoosmotrophic organisms, in contrast, assimilate organic carbon and nutrients in dissolved form. The heterotrophic prokaryotes fall into this category. They share this feature with a number of eukaryotes including the eumycotic fungi (Basidiomycota, Ascomycota, Zygomycota, Chytridiomycota, and Deuteromycora [scc, e.g., references 16 and 40|) and the phylogenetically unrelated oomycetous prousts (Oomycota), thraustochytrids, and labyrinthulids (Labyrinthulomycota) (44, 97), the last of which are also partially phagotrophic.&lt;br /&gt;Although eukaryotic organoosmotrophs have a polyphyletic origin, they are commonly considered to belong to the fungi, sensu lato, a group of organisms that mostly contains mycelial growth forms (filamentous fungi) but also includes some nonmycelial forms such as yeasts and chytrids. Filamentous or mycelial fungi are ubiquitous in aquatic environments and exhibit a remarkable diversity (14, 38, 61, 63, 86, 87, 97, 159, 167, 178). They occur as pathogens, commensals, or mutualistic symbionts of algae, vascular plants, and animals in both pelagic and benthic systems (44, 72, 108, 190), and they may mediate a wide variety of biogeochemical transformations (179). Their predominant habitat, however, is plant litter accumulating within land-water transition zones such as coastal marine areas; streams, rivers, and estuaries receiving litter from the riparian vegetation; the littoral zones of lakes; and other freshwater wetlands (61). The implication of this occurrence and the characteristic penetrative growth form (115, 118) is that mycelial fungi are primarily found within opaque solid substrates. In consequence, their hyphae are neither immediately visible nor easily separable from the plant tissue without significant destruction taking place (112). Here lies the major challenge for the investigator who wants to assess the community structure, productivity, and activity of these organisms in their natural environment. [...]
Screening asymptomatic patients at high risk for colon cancer with full colonoscopy (1987)

To evaluate the reliability of screening only the distal colon in patients at high risk for colonic cancer, the endoscopic findings of 49 completely asymptomatic patients who underwent colonoscopy based solely on a positive family history of colonic cancer (average age, 54.5 years) were reviewed. Polypoid lesions were present in 31 (63.3 percent). Thirty-three polyps in 13 patients were larger than 1 cm, including two invasive cancers. Eleven patients (22.4 percent) had polyps proximal to 40 cm only and would not have been identified on examination of the distal bowel alone. The predictive accuracy of rectosigmoid screening in this population is 78 percent. Initial screening of patients at high risk for colonic cancer should include full colonoscopy. The extent of follow-up examinations is then based on endoscopic findings.
Mapping antigenic domains expressed by Chlamydia trachomatis major outer membrane protein genes. (1988)

Chlamydia trachomatis is an obligate prokaryotic intracellular pathogen of humans that infects mucosal epithelial cells. Exposed domains of its major outer membrane protein (MOMP) are both serotyping and protective antigenic determinants. To identify these domains, we have cloned and epitope-mapped the genes of serovars A, C (C serogroup) and L2, B (B serogroup) with a panel of monoclonal antibodies (mAbs). Predominantly conserved regions of the genes of both serogroups are interspersed with four short variable domains (I-IV). Recombinant phage clones expressing specific MOMP antigenic determinants revealed that protective serotype-specific recognized epitopes in variable domains I and II. Protective subspecies and serogroup-specific mAbs recognized overlapping determinants in variable domain IV near the C terminus. A nonprotective species-specific mAb mapped to an invariant peptide of nine residues contained within variable domain IV. In the intact chlamydial organism of serovar B, variable domains II and IV were susceptible to proteolytic digestion, whereas both N and C termini were protected. These results suggest an arrangement of MOMP in the outer membrane in which three of the four variable domains are exposed to the outside and in which both N and C termini are presumably oriented toward the periplasmic space. This molecular analysis of MOMP antigenic determinants and their surface topology on intact chlamydiae will be useful toward the development of a recombinant subunit or synthetic chlamydial vaccine.
제18대 대통령선거와 회고적 투표: 왜 제18대 대통령선거에서 집권정부에 대한 회고적 평가가 중요한 영향을 미치지 못했나? (2013)

본 논문의 목적은 지난 제18대 대통령선거에서 집권정부의 국정운영에 대한 부정적인 회고적 평가가 투표선택에 중요한 영향을 미치지 못한 이유를 분석하는 것이다. 이명박 정부의 국정운영 실적에 대한 평가가 매우 부정적이었음에도 불구하고 제18대 대통령선거에서 여당의 박근혜 후보가 승리를 거둔 결과는 집권정부에 대한 회고적 평가가 유권자의 후보선택에 미친 영향력이 제한적이었다는 점을 나타낸다. 이 논문은 두 가지 핵심 가설을 제시하고 이를 동아시아연구원, 중앙일보, SBS, 한국일보가 공동으로 수행한‘2012 총선대선 패널조사(KEPS)’자료의 경험적 분석을 통해 검증한다. 첫 번째 가설은 야당 문재인 후보와 비교하여 박근혜 후보의 국정운영 능력을 상대적으로 높게 평가하고 이에 기초하여 후보를 선택한 소위 전망적 투표를 한 유권자가 많았기 때문에 박근혜 후보가 당선되었다는 것이다. 두 번째 가설은 야당 문재인후보가 노무현 정부에서 핵심적 역할을 했기 때문에 여당이 제기한‘노무현 정부 재심판론,’즉 노무현 정부에 대한 부정적인 회고적 평가가 박근혜 후보의 당선에 영향을 미쳤다는 것이다. 경험적 분석의 결과, 주요한 사회적 변인들을 모두 통제한 상태에서도 박근혜 후보에 대한 전망적 평가와 그녀에 대한 개인적 선호도가 투표 결정에 큰 영향을 끼친 것으로 나타났다. 또한 노무현 정부에 대한 회고적 평가가 박근혜 후보로의 투표결정에 상당한 영향을 끼친 것으로 확인되었다. 즉‘노무현 정부 재심판’의 주장이 상당수 유권자에게 수용된 것으로 보인다. 반면 이명박 대통령에 대한 비판적 태도와 낮은 지지도는 박근혜 후보 선택에 큰 장애가 되지 못한것으로 나타났다. 이러한 분석결과는 현직 대통령이나 정부가 아닌, 이전의 대통령이나 정부도 유권자들의 재(再)회고와 평가의 대상이 될 수도 있다는 점에서 의미 있는 시사점을 제시한다.
The Paradox of the Low-Renin State in Diabetic Nephropathy (1999)

Although diabetic nephropathy is often a low renin state, the renin system appears to be implicated in its pathogenesis. In this study, it was hypothesized that the low plasma renin activity (PRA) is misleading, masking and perhaps reflecting an activated intrarenal renin system. PRA and renal vascular responses (inulin and para-aminohippurate clearance) to graded doses of an angiotensin II (AngII) antagonist, irbesartan, were assessed in eight healthy volunteers and 12 patients with type 2 diabetes mellitus and nephropathy on a 10 mmol Na intake, to activate the renin system. Basal PRA was suppressed in type 2 diabetes mellitus compared with the healthy subjects (0.58 +/- 0.14 versus 1.58 +/- 0.28 ng/L per s, mean +/- SEM; P < 0.01). Despite the low PRA, renal perfusion rose more in response to irbesartan in type 2 diabetes mellitus (714 +/- 83 to 931 +/- 116 ml/min; P = 0.002) than normal (624 +/- 29 to 772 +/- 49 ml/min; P = 0.008). The youngest patients were hyperfiltrating and showed the largest rise in renal plasma flow in response to irbesartan, whereas renal plasma flow rose less and GFR fell in patients with low basal GFR. PRA rose in response to irbesartan more gradually in the patients with type 2 diabetes mellitus, but ultimately matched the normal response. To account for the apparent paradox of a heightened renal hemodynamic response to an AngII antagonist in the face of a low PRA in type 2 diabetes mellitus, and the rise in PRA following the AngII antagonist, it is proposed that there is increased intrarenal AngII production in type 2 diabetes mellitus. This increase could account for suppressed circulating renin, the exaggerated renal vasodilator response to irbesartan, and the therapeutic effectiveness of interrupting the renin system in diabetic nephropathy.
Brimonidine versus dapiprazole: Influence on pupil size at various illumination levels (2005)

Pupil mydriasis at scotopic illumination levels was reduced by both drugs in a similar fashion. Because of the slightly stronger effect of brimonidine, application of this agent 20 minutes before activities in dimly lit areas or at night may be recommended for photic phenomena following refractive surgery.
Core/Shell Semiconductor Nanocrystals (2009)

Colloidal core/shell nanocrystals contain at least two semiconductor materials in an onionlike structure. The possibility to tune the basic optical properties of the core nanocrystals, for example, their fluorescence wavelength, quantum yield, and lifetime, by growing an epitaxial-type shell of another semiconductor has fueled significant progress on the chemical synthesis of these systems. In such core/shell nanocrystals, the shell provides a physical barrier between the optically active core and the surrounding medium, thus making the nanocrystals less sensitive to environmental changes, surface chemistry, and photo-oxidation. The shell further provides an efficient passivation of the surface trap states, giving rise to a strongly enhanced fluorescence quantum yield. This effect is a fundamental prerequisite for the use of nanocrystals in applications such as biological labeling and light-emitting devices, which rely on their emission properties. Focusing on recent advances, this Review discusses the fundamental properties and synthesis methods of core/shell and core/multiple shell structures of II-VI, IV-VI, and III-V semiconductors.