gebhart/patrepeval huggingface dataset:
Bayesian adaptive estimation of the contrast sensitivity function: The quick CSF method (2010)

The contrast sensitivity function (CSF) predicts functional vision better than acuity, but long testing times prevent its psychophysical assessment in clinical and practical applications. This study presents the quick CSF (qCSF) method, a Bayesian adaptive procedure that applies a strategy developed to estimate multiple parameters of the psychometric function (A. B. Cobo-Lewis, 1996; L. L. Kontsevich & C. W. Tyler, 1999). Before each trial, a one-step-ahead search finds the grating stimulus (defined by frequency and contrast) that maximizes the expected information gain (J. V. Kujala & T. J. Lukka, 2006; L. A. Lesmes et al., 2006), about four CSF parameters. By directly estimating CSF parameters, data collected at one spatial frequency improves sensitivity estimates across all frequencies. A psychophysical study validated that CSFs obtained with 100 qCSF trials ( approximately 10 min) exhibited good precision across spatial frequencies (SD < 2-3 dB) and excellent agreement with CSFs obtained independently (mean RMSE = 0.86 dB). To estimate the broad sensitivity metric provided by the area under the log CSF (AULCSF), only 25 trials were needed to achieve a coefficient of variation of 15-20%. The current study demonstrates the method's value for basic and clinical investigations. Further studies, applying the qCSF to measure wider ranges of normal and abnormal vision, will determine how its efficiency translates to clinical assessment.
Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems (2001)

Short interfering RNAs (siRNAs) are double-stranded RNAs of approximately 21-25 nucleotides that have been shown to function as key intermediaries in triggering sequence-specific RNA degradation during posttranscriptional gene silencing in plants and RNA interference in invertebrates. siRNAs have a characteristic structure, with 5'-phosphate/3'-hydroxyl ends and a 2-base 3' overhang on each strand of the duplex. In this study, we present data that synthetic siRNAs can induce gene-specific inhibition of expression in Caenorhabditis elegans and in cell lines from humans and mice. In each case, the interference by siRNAs was superior to the inhibition of gene expression mediated by single-stranded antisense oligonucleotides. The siRNAs seem to avoid the well documented nonspecific effects triggered by longer double-stranded RNAs in mammalian cells. These observations may open a path toward the use of siRNAs as a reverse genetic and therapeutic tool in mammalian cells.
The process zone: A microstructural view of fault growth (1998)

The deformation associated with several small, brittle faults was investigated on both microscopic and macroscopic scales. While the dominant macroscopic structures are solution cleavage planes and secondary shear fractures, the dominant microscopic deformation structures are healed tensile microfractures. The fault‐related microfractures display densities and orientations distinct from the background microfracture population. These densities and orientations are consistent with formation within the altered stress fields of propagating shear fracture tips. This microfracture population is used to define the fault process zone associated with growth of the macroscopic fault plane. Process zone microfractures show logarithmic density increases with proximity to the fault, a constant maximum density that is independent of fault length, and orientations which can be used to infer the direction of propagation of the fault plane. The width of the process zone scales linearly with fault length with a proportionality constant of the order of 10 −2 .
Chronic obstructive pulmonary disease overview: prevalence, pathogenesis, and treatment. (2004)

An insidious disorder that is asymptomatic early, COPD (the preferred term for patients with chronic bronchitis and emphysema) prevalence has increased in recent decades, adding a significant burden to patients and the health care system. COPD, an inflammatory disorder secondary to the chronic inhalation of principally tobacco smoke, induces a progressive deterioration in pulmonary function with a marked increase in morbidity and mortality over time. The signs and symptoms of COPD, which appear in many patients only after forced expiratory volume in 1 second (FEV1) is <50% predicted, should not be confused with asthma, because these two diseases display grossly different inflammatory processes, etiologies, clinical courses, responses to treatment, and outcomes. The effective management of COPD relies primarily on early identification, changing smoking habits, and the use of bronchodilators to improve pulmonary function, symptoms, acute exacerbation rate, quality of life, mortality, and comorbidities. With early detection and aggressive treatment, the natural history of this disease can be improved. Office spirometry for all smokers and ex-smokers as well as those with respiratory symptoms is mandatory as a means of achieving early diagnosis and improving long-term outcomes.
Increased expression of chemokine receptor CCR3 and its ligands in ulcerative colitis: the role of colonic epithelial cells inin vitrostudies (2010)

Human colonic epithelial cells express T helper type 1 (Th1)-associated chemoattractants, yet little is known about the production of Th2-associated chemoattractants. CCL11/eotaxin-1, CCL24/eotaxin-2 and CCL26/eotaxin-3 are known to attract CCR3-expressing, Th2-polarized lymphocytes. We studied constitutive and inflammation-induced expression and production of CCR3 together with its ligands in the colon and peripheral blood of patients with inflammatory bowel disease (IBD) by flow cytometry, reverse transcription–polymerase chain reaction (RT–PCR) and enzyme-linked immunosorbent assay (ELISA). We further defined the regulated expression of these chemokines by RT–PCR and ELISA using cultured human epithelial cell lines. A higher fraction of peripheral T lymphocytes were found to be positive for CCR3 in patients with ulcerative colitis (UC) compared to Crohn’s disease (CD), while almost no CCR3(+) T cells were found in normal controls (NC). Similarly, higher and more frequent expression of CCR3 was observed in colonic biopsies from patients with UC, regardless of the disease activity, when compared to CD or NCs. Serum CCL11/eotaxin-1 was increased significantly in UC (306 ± 87 pg/ml) and less so in CD (257 ± 43 pg/ml), whereas CCL24/eotaxin-2, and CCL26/eotaxin-3 were increased only in UC. Colonic expression of the three chemokines was minimal in NCs but high in inflammatory bowel diseases (especially UC) and was independent of disease activity. Th2, and to a lesser extent Th1, cytokines were able to induce expression and production of all three eotaxins from colonic epithelial cells in culture. CCR3 and ligands over-expression would appear to be a characteristic of UC. The production of CCR3 ligands by human colonic epithelial cells suggests further that epithelium can play a role in modulating pathological T cell-mediated mucosal inflammation.
Online Anomaly Prediction for Robust Cluster Systems (2009)

In this paper, we present a stream-based mining algorithm for online anomaly prediction. Many real-world applications such as data stream analysis requires continuous cluster operation. Unfortunately, today's large-scale cluster systems are still vulnerable to various software and hardware problems. System administrators are often overwhelmed by the tasks of correcting various system anomalies such as processing bottlenecks (i.e., full stream buffers), resource hot spots, and service level objective (SLO) violations. Our anomaly prediction scheme raises early alerts for impending system anomalies and suggests possible anomaly causes. Specifically, we employ Bayesian classification methods to capture different anomaly symptoms and infer anomaly causes. Markov models are introduced to capture the changing patterns of different measurement metrics. More importantly, our scheme combines Markov models and Bayesian classification methods to predict when a system anomaly will appear in the foreseeable future and what are the possible anomaly causes. To the best of our knowledge, our work provides the first stream-based mining algorithm for predicting system anomalies. We have implemented our approach within the IBM System S distributed stream processing cluster, and conducted case study experiments using fully implemented distributed data analysis applications processing real application workloads. Our experiments show that our approach efficiently predicts and diagnoses several bottleneck anomalies with high accuracy while imposing low overhead to the cluster system.
Sub-Half-Micron Lithography for ULSIs (2000)

1. Introduction Masao Fukuma 2. Optical lithography Kunihiko Kasama, Shinji Okazaki, Hisatake Sano and Wataru Wakamiya 3. X-ray lithography Kimiyoshi Deguchi, Teruo Hosokawa, Sunao Ishihara and Katsumi Suzuki 4. Electron beam lithography Takayuki Abe, Koichi Moriizumi, Yukinori Ochiai, Norio Saitou, Tadahiro Takigawa and Akio Yamada 5. Ion beam lithography Masanori Komuro and Shinj Matsui 6. Resists Hiroshi Ban, Tadayoshi Kokubo, Makoto Nakase and Takeshi Ohfuji 7. Metrology, defect inspection and repair Tadahito Matsuda, Toru Tojo and Seiichi Yabumoto Index.
The nutritive value of barley, maize, oats and wheat for poultry (1974)

Synopsis The crude compositions of samples of barley, maize, oats and wheat are given together with a more detailed analysis of the protein and carbohydrate fractions. The nutritional potential of these samples to the laying hen has been investigated using colostomised birds. By regression analysis of absorption on intake, the true digestibility of the crude protein was calculated to be 83.6, 82.2, 85.0 and 847%, that of the crude fat 92.5, 94.9, 95.0 and 92.5% and that of the carbohydrate 73.0, 87.2, 52.1 and 81.1% for barley, maize, oats and wheat respectively. The true digestibility coefficients of some amino acids are also given. The classical meta‐bolisable energy values of the barley, maize, oat and wheat samples studied were found to be 11.12, 13.21, 11.05 and 12.18 MJ/kg (2.66, 3.16, 2.64 and 2.91 kcal/g) respectively. It is concluded that there is scope for improving the digestibility of the protein in all the cereals studied and that digestibility of the non‐starch carbohydrate fraction is very low.
New Strategies in Pancreatic Cancer: Emerging Epidemiologic and Therapeutic Concepts (2010)

Pancreatic cancer (PC) is a highly lethal disease with complex etiology involving both environmental and genetic factors. Although cigarette smoking is known to explain 25% of cases, data from recent studies suggest that obesity and long-term type II diabetes are two major modifiable risk factors for PC. Furthermore, obesity and diabetes seem to affect the clinical outcome of patients with PC. Understanding the mechanistic effects of obesity and diabetes on the pancreas may identify new strategies for prevention or therapy. Experimental and epidemiologic evidence suggests that the antidiabetic drug metformin has protective antitumor activity in PC. In addition to insulin resistance and inflammation as mechanisms of carcinogenesis, obesity and diabetes are linked to impairments in endothelial function and coagulation status, which increase the risks of thrombosis and angiogenesis and, in turn, the risk of PC development and progression. The associations of the ABO blood group gene and NR5A2 gene variants with PC discovered by recent genome-wide association studies may link insulin resistance, inflammation, and thrombosis to pancreatic carcinogenesis. These exciting findings open new avenues for understanding the etiology of PC and provide opportunities for developing novel strategies for prevention and treatment of this disease.
MIME E-mail Encapsulation of Aggregate Documents, such as HTML (MHTML) (1997)

This document specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements. Please refer to the current edition of the "Internet Official Protocol Standards" (STD 1) for the standardization state and status of this protocol. Distribution of this memo is unlimited.
Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor (1995)

Matrix metalloproteinases are a family of zinc endopeptidases involved in tissue remodeling. They have been implicated in various disease processes including metastasis, joint destruction, and neurodegeneration. Human neutrophil collagenase (HNC, MMP-8) represents one of the three "interstitial" collagenases that cleave triple-helical collagens types I, II, and III. Its 163-residue catalytic domain (Met80 to Gly242) has been expressed in Escherichia coli and crystallized as a noncovalent complex with the hydroxamate inhibitor batimastat. The crystal structure, refined to 2.1 A, demonstrates that batimastat binds to the S1-S2' sites and coordinates to the catalytic zinc in a bidentate manner via the hydroxyl and carbonyl oxygens of the hydroxamate group. The batimastat-collagenase complex is described in detail, and the activities of batimastat analogues are discussed in the light of the protein-inhibitor interactions revealed by the crystallography studies.
Network management of wireless tactical networks (2002)

This paper presents a network layer protocol developed for tactical multimedia networks in the forward area. The proposed network is an autonomous fully distributed wireless ATM network. The structure of the proposed network is hierarchical and allows for rapid deployment and dynamic reconfiguration of wireless stations. Nodes are organized into clusters. The cluster heads are analogous to the base stations in a conventional ATM and they act as the local coordinators to support services that include conventional data applications as well as multimedia (video, voice and data) applications with QoS (quality-of-service) guarantees. The proposed protocols are also intended to provide seamless internetworking with other wired ATM local and wide area networks. The algorithms are distributed for simple implementation and ease of mobility management. A wireless VP/VC concept is described to provide ATM cell routing and connections in the network. Routing and the provision for efficient utilization of the available bandwidth are major problems for supporting multimedia traffic in a wireless network. Call management, network management, and signaling are designed for simplicity. Restoration schemes are also proposed to resolve the connectivity problems associated with link or node failures.
An Integrated Model for Whether, Who, When, and How Much in Internet Auctions (2005)

We develop a general parametric modeling framework for bidding behavior in Internet auctions. Toward this end, we incorporate and model simultaneously four key components of the bidding process under our integrated framework: Whether an auction will have a bid at all, (if so) who has bid, when they have bid, and how much they have bid over the entire sequence of bids in an auction. This integrated framework is based on a single latent time-varying construct of consumer willingness to bid (WTB), which bidders have and update for a particular auction item over the course of the auction duration. Our modeling approach is also based on a simple yet very general bidding premise: The observed bidder's latent WTB at a specific bid is greater than the outstanding bid; yet, WTB is unconstrained for all other potential bidders. In this manner, we impose no structural assumption on bidder rationality or equilibrium behavior; instead, deriving our model using a probabilistic modeling paradigm. We describe in detail the advantages that our reducted-form approach allows us, and the limitations such an approach also entails. Using a database of notebook auctions from one of the largest Internet auction sites in Korea, we demonstrate that this general (yet parsimonious) model captures the key behavioral aspects of bidding behavior. Furthermore, substantively, through a data-windowing procedure to assess the set of potential bidders for a given auctioned item, we provide a valuable tool for managers at auction sites to conduct their customer relationship management efforts which require them to evaluate the goodness (whether) of the listed auction items and the goodness (who, when, and how much to bid) of the potential bidders in their Internet auctions.
Systemic administration of recombinant interleukin 2 stimulates in vivo lymphoid cell proliferation in tissues. (1985)

Recent work in our laboratory has demonstrated that the repeated injections of high doses of recombinant interleukin 2 (IL 2) can dramatically reduce the number of established pulmonary and hepatic metastases and the growth of intradermal tumors in a variety of murine tumor models. We have thus undertaken studies to define the mechanisms underlying these in vivo effects of IL 2. Using an in vivo DNA-labeling technique in which we employed 5-[125I]iodo-2'-deoxyuridine (125IUdR), we examined the in vivo cell proliferation in the tissues of mice treated with IL 2. A proliferation index (PI) was calculated by dividing the raw counts per minute (cpm) of tissues in IL 2-treated mice by the cpm in corresponding tissues of control animals. At an IL 2 dose of 6000 U given i.p. three times a day, the highest 125IUdR incorporation was seen in the lungs, liver, spleen, kidneys, and mesenteric lymph nodes (PI = 6.9, 6.9, 5.1, 7.1, 24.6, respectively, at 5 days). The amount of lymphoid proliferation in these organs was a direct function of the dose of IL 2 administered. Other tissues including thymus, intestines, skin, and hind limb showed no significant increase in 125IUdR uptake even after host treatment with the highest doses of IL 2. Blood and brain demonstrated intermediate incorporation of the radiolabel. Preirradiation of the host largely eliminated the proliferative response to IL 2. Histologic studies of normal and irradiated mice receiving IL 2 corroborated the result of the 125IUdR findings. In normal IL 2-treated mice, large collections of activated lymphoid cells were seen, most prominently in the lungs, liver, and kidneys, whereas markedly decreased lymphoid proliferation was evident histologically in preirradiated mice. A fluorescein-labeled monoclonal antibody directed against the Thy-1.2 surface determinant was used to identify these dividing cells in frozen tissue sections as T lymphoid cells. Activated lymphocytes isolated from the lungs, liver, spleen, and mesenteric lymph nodes of IL 2-treated mice demonstrated significant lysis of a fresh murine sarcoma target in short-term 51Cr-release assays. These studies demonstrate that the systemic administration of recombinant IL 2 causes in vivo activation and proliferation of host lymphoid cells and has important implications for the adoptive immunotherapy of tumors.
cDNA cloning of a human mRNA preferentially expressed in hematopoietic cells and with homology to a GDP-dissociation inhibitor for the rho GTP-binding proteins. (1993)

We have identified the mRNA for a human gene, denoted D4, which is expressed at very high levels in hematopoietic cell lines and in normal cells of lymphoid and myeloid origin. The 1.5-kb transcript is absent or detectable only at low levels in nonhematopoietic tissues. D4 encodes a 201-amino acid protein with homology to rhoGDI, an inhibitor of GDP dissociation for the ras-homologous protein rho. D4 might function also as a regulator of guanine nucleotide exchange for small GTP-binding proteins. A homologous transcript of similar size is also preferentially expressed in murine hematopoietic tissues. When totipotent murine embryonic stem cells develop in vitro into hematopoietic cells, the gene is activated with the onset of hematopoiesis. When hematopoietic cell lines are induced to differentiate, the expression of D4 is modulated. Thus, D4 appears to be a developmentally regulated gene. Its preferential expression in hematopoietic cells indicates that D4 likely plays some significant role in the growth and differentiation processes of hematopoietic cells. This significance is underscored by increasing evidence for the involvement of regulators of G proteins in clinical diseases.
Muscle as a putative producer of acid alpha-glucosidase for glycogenosis type II gene therapy (2002)

Glycogenosis type II (GSD II) is a lysosomal disorder affecting skeletal and cardiac muscle. In the infantile form of the disease, patients display cardiac impairment, which is fatal before 2 years of life. Patients with juvenile or adult forms can present diaphragm involvement leading to respiratory failure. The enzymatic defect in GSD II results from mutations in the acid alpha-glucosidase (GAA) gene, which encodes a 76 kDa protein involved in intralysosomal glycogen hydrolysis. We previously reported the use of an adenovirus vector expressing GAA (AdGAA) for the transduction of myoblasts and myotubes cultures from GSD II patients. Transduced cells secreted GAA in the medium, and GAA was internalized by receptor-mediated capture, allowing glycogen hydrolysis in untransduced cells. In this study, using a GSD II mouse model, we evaluated the feasibility of GSD II gene therapy using muscle as a secretary organ. Adenovirus vector encoding AdGAA was injected in the gastrocnemius of neonates. We detected a strong expression of GAA in the injected muscle, secretion into plasma, and uptake by peripheral skeletal muscle and the heart. Moreover, glycogen content was decreased in these tissues. Electron microscopy demonstrated the disappearance of destruction foci, normally present in untreated mice. We thus demonstrate for the first time that muscle can be considered as a safe and easily accessible organ for GSD II gene therapy.
Restriction of lentivirus in monkeys (2002)

Retroviruses are able to cross species barriers and have done so many times throughout evolution. Perhaps as a consequence, dominant mechanisms have arisen to block infection by murine retroviruses in mice (restriction factor Fv1) and humans (restriction factor Ref1), as well as in other mammals. Here we describe a block to HIV and simian immunodeficiency virus in monkeys. Like previously described restrictions the block is saturable and gives rise to multiple-hit infection kinetics. Furthermore, like restriction of murine leukemia virus in humans, the block is before reverse transcription. Intriguingly, African green monkey cells are able to block both HIV and simian immunodeficiency virus, and each virus is able to saturate and abrogate the restriction of the other, suggesting that a common factor is responsible.