gebhart/patrepeval huggingface dataset:
Optimal nonsingular control of fed‐batch fermentation (1991)

Presented is a new simple method for multidimensional optimization of fed-batch fermentations based on the use of the orthogonal collocation technique. Considered is the problem of determination of optimal programs for fermentor temperature, substrate concentration in feed, feeding profile, and process duration. By reformulation of the state and control variables is obtained a nonsingular form of the optimization problem which has considerable advantage over the singular case since a complicated procedure for determination of switching times for feeding is avoided. The approximation of the state variables by Lagrange polynomials enables simple incorporation of split boundary conditions in the approximation, and the use of orthogonal collocations provides stability for integration of state and costate variables. The interpolation points are selected to obtain highest accuracy for approximation of the objective functional by the Radau-Lobatto formula. The control variables are determined by optimization of the Hamiltonian at the collocation points with the DFP method. Constraints are imposed on state and control variables.The method is applied for a homogeneous model of fermentation with volume, substrate, biomass, and product concentrations as the state variables. Computer study shows considerable simplicity of the method, its high accuracy for low order of approximation, and efficient convergence.
Optimization for allocating BEV recharging stations in urban areas by using hierarchical clustering (2010)

The Battery Electric Vehicle (BEV) prototypes are evolving into a reality in a foreseeable future. Before BEV can embark on a mass adoption by road commuters, a new infrastructure for battery charging will have to be ready in place. By 2015, access to BEV charging will be available at nearly one million charge points in the United States, as claimed by CleanMPG. Early BEV adopters will primarily charge their vehicles at home, in their private garages. However, for many Asia-Pacific regions where people live in concrete ghettos, public charging will play a more central role due to reduced access to convenient home charging. This research focuses on planning BEV charging locations to be installed in urbanized areas where they are usually characterized by dense traffic concentrations, restricted street spaces and other complex factors such as the distribution of power grids. We proposed a two-steps model that first quantified the road information into data points, and subsequently they are converged into 'demand clusters' over an urbanized area by hierarchical clustering analysis. Optimization techniques then applied on the demand clusters with the aim of meeting the supplies and demands, while at the same time certain constraints and cost factors are considered. The model is believed to be an important decision-support tool for city planning and BEV charging stations allocation.
Activity of in situ middle cervical ganglion neurons in dogs, using extracellular recording techniques (1985)

Neuronal activity in the in situ middle cervical ganglion of dogs was investigated using extracellular recording techniques. The recorded action potentials were frequently active during specific phases of the cardiac cycle, particularly during systole, and this activity persisted following acute decentralization of the ganglion. The activity of these action potentials was modified when systemic arterial pressure was altered by isoproterenol, noradrenaline, adrenaline, or partial occlusion of the aorta, whether in the intact or acutely decentralized preparation. These neurons were active between systolic pressures of 70 and 180 mmHg (1 mmHg = 133.322 Pa). Action potentials were frequently modified by mechanical distortion of the superior vena cava, ventricular epicardium, or adventitia of the aorta, whether the preparation was acutely decentralized or not. Seventy percent of these action potentials were unaffected by stimulation (1 ms, 4 V, 0.5 Hz) of a cardiopulmonary nerve and 27% were suppressed by such stimulation. Five of the neurons were activated by such stimulation. It is presumed that the latter neurons had axons in a cardiopulmonary nerve and most likely were efferent sympathetic postganglionic neurons. Sixty-three percent of these spontaneously active phase-locked units were modified by stimulation of a ramus or an ansa. It is postulated that some of the neurons in the middle cervical ganglia can be modified by afferent axons arising from receptors in thoracic organs, in particular from the great vessels and heart, whether in an intact or acutely decentralized preparation. The majority of these neurons are presumed not to be afferent neurons or efferent postganglionic neurons, as they are not activated directly by electrical stimulation of axons in cardiopulmonary nerves. Rather they are presumed to be interneurons. These results lend support to the thesis that considerable integration of neuronal activity related to thoracic cardiovascular dynamics occurs within the middle cervical ganglia of dogs.
Intralipid as Treatment for Recurrent Unexplained Abortion? (1994)

The evidence suggests that Intralipid might be an effective treatment for human recurrent miscarriages, and injection into women who may become pregnant has been found ethically acceptable at one university center. Comparison of Intralipid to partner leukocyte immunotherapy or IVIG would be worthwhile. For adequate statistical power, this would require a large, multicenter, prognostically stratified randomized controlled trial and could be accomplished via the Recurrent Miscarriage Immunotherapy Trialists Group network.
Determinstic lateral displacement mems device for continuous blood cell separation (2005)

This work presents a new MEMS device which uses deterministic lateral displacement for the continuous separation of leukocytes (white blood cells) and erythrocytes (red blood cells). By running blood cells in laminar flow through an array of columnar obstacles, deterministic lateral displacement asserts that the path a cell follows is determined by its size. The system consists of PDMS channels with posts on glass slides. An effective separation region of 7 mm by 1.8 mm is achieved on a 1 cm by 1 cm chip. A 420 /spl mu/m lateral separation was achieved for 5 /spl mu/m and 10 /spl mu/m beads. The critical particle size for separation was found experimentally to be 8 /spl mu/m, concluded from our results using 5 /spl mu/m, 7 /spl mu/m, 8 /spl mu/m and 10 /spl mu/m polystyrene beads. Diluted whole blood and blood fraction of concentrated leukocytes were also tested with the devices in agreement with blood count results. Problem of blood cell stiction to device surfaces was investigated.
Cell interactions and cytokines in transplantation immunity. (1995)

Peripheral T cells usually harbor clones that can directly recognize allogeneic HLA molecules in association with hitherto undefined allogeneic peptides. However, recognition does not lead to activation of allograft immunity, unless the allogeneic cells are professional ISCs. In the absence of such cells in the graft, activation of specific alloimmunity might occur indirectly by host ISCs presenting graft-derived allogeneic peptides. Such peptides are thought to often be derived from allogeneic HLA molecules themselves. A local inflammation followed by activation of endothelial cells could facilitate the migration of immunocompetent cells into the graft parenchyma and stimulation by dendritic cells in the graft. A local inflammation is believed to be induced by ischemic damage to cells in the graft, to postoperative aseptic inflammation associated with wound healing and repair, or by ongoing local infection. Naive or virgin T cells primarily migrate to secondary lymphoid organs and specific subsets of T cells traffic selective organs such as the gut or lymph nodes. However, memory T cells extravasate to sites of local inflammation. Therefore, prior T-cell alloimmunity, which might be the result of immunity against cross-reactive self-HLA restricted foreign peptides, as well as a local inflammatory reaction in the graft, caused by tissue damage or mediated by preexisting low levels of noncytotoxic antibodies, might facilitate graft rejection.
Microsatellite Instability in Sporadic Endometrial Carcinoma (1994)

The RER+ phenotype is frequently present in sporadic endometrial cancers and is expressed before and during clonal expansion. The underlying mutator mutations are probably heterogeneous, since the RER+ phenotypes were diverse. The absence of altered microsatellites in adjacent normal endometrium demonstrates that the expression of the RER+ phenotype is limited to neoplastic tissue. The bulk of the microsatellite alterations appeared to be acquired prior to clonal expansion, suggesting that expression of the underlying genomic instability contributes to, and is not a consequence of, transformation.
Prognostic Significance of Vascular Endothelial Growth Factor Protein Levels in Oral and Oropharyngeal Squamous Cell Carcinoma (2000)

In this cohort, VEGF positivity was the most significant predictor of poor prognosis. VEGF status may prove to be an important prognostic factor in head and neck cancer.
A visualization method of program dependency graph for identifying extract method opportunity (2011)

Refactoring is important for efficient software maintenance. However, tools supports are highly required for refactoring because manual operations of refactoring are troublesome and error prone. This paper proposes a technique that suggests Extract Method candidates automatically. Extract Method refactoring is to create a new method from a code fragment in an existing method. Previous research efforts showed that the Extract Method refactoring is often performed prior to other refactorings, so that it is important to support Extract Method refactoring. Previous studies have proposed methods that suggest Extract Method candidates based on linage or complexity. However it is originally desirable to divide methods based on their functionalities. This paper uses the strength of data connection between sentences in the source code. We deem that strongly-connected data expresses a single function. This paper proposes a technique that suggests Extract Method candidates based on strongly-connected data.
Blockade of CD40 ligand-CD40 interaction impairs CD4+ T cell-mediated alloreactivity by inhibiting mature donor T cell expansion and function after bone marrow transplantation (1997)

Alloreactive T cells require costimulatory signals via CD40 ligand (CD40L). The tissue-destructive properties of allogeneic CD4+ but not CD8+ T cells were inhibited by anti-CD40L mAb. Fewer CD4+ thoracic duct lymphocytes (TDL) were obtained in mAb-treated recipients. Kinetic studies revealed that CD4+ T cell expansion was reduced or delayed which may account, in part, for the partial graft-vs-host disease protective effect of anti-CD40L mAb. TDL were found to have diminished anti-host-specific proliferative responses. The frequency of donor TDL and splenocytes that expressed the Th1 cytokines IL-2, IL-12 p40, and IFN-gamma mRNA was markedly diminished in mAb-treated recipients, demonstrating that Th1-driven alloresponses were susceptible to CD40L targeting. Perforin mRNA-expressing T cells were undetectable in mAb-treated recipients, consistent with reduced in vivo lethality after the adoptive transfer of allogeneic CD4+ T cells. Similar findings were observed in both B cell-replete or -deficient recipients, indicating that allogeneic T cell expansion and priming can be sustained by a non-B cell, CD40+ host cell population. Mice receiving CD40L-deficient allogeneic CD4+ T cells had survival rates comparable to the rates of those given anti-CD40L mAb treatment. Because anti-CD40L mAb also was found to prevent host anti-donor-mediated marrow allograft rejection, in vivo blockade of CD40L-CD40 interactions may provide a highly beneficial approach to improving the outcome of allogeneic bone marrow transplantation.
Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability (2020)

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a large impact on global health, travel, and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent coronavirus disease 2019 (COVID-19) patients using a SARS-CoV-2 stabilized prefusion spike protein. These antibodies had low levels of somatic hypermutation and showed a strong enrichment in VH1-69, VH3-30-3, and VH1-24 gene usage. A subset of the antibodies was able to potently inhibit authentic SARS-CoV-2 infection at a concentration as low as 0.007 micrograms per milliliter. Competition and electron microscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In addition to providing guidance for vaccine design, the antibodies described here are promising candidates for COVID-19 treatment and prevention.
Histopathological Studies on Senile Plaques and Cerebral Amyloid Angiopathy in Aged Cynomolgus Monkeys (1994)

The incidence and morphological characteristics of senile plaque and amyloid angiopathy in the cerebrum of six aged cynomolgus monkeys (Macaca fascicularis), 20 to 29 years old, were studied histopathologically and immunohistochemically. By periodic acid methenamine silver stain (PAM) and alkaline Congo red stain, senile plaques were detected in 5 out of 6 cases, and 3 of them were positive for amyloid in the wall of capillaries and arterioles in the cerebral cortex. Senile plaques were classified into three types. Mature plaques, including classical and primitive types, were more frequently observed than the immature diffuse type. Senile plaques were often seen in the cortex of temporal lobe, putamen and head of caudate nucleus. Since mature types of senile plaques were seen frequently around vascular amyloid deposition and no amyloid angiopathy was detected in the areas without senile plaques, the close relation between senile plaque of the mature type and amyloid angiopathy might be considered. All senile plaques and amyloid angiopathy were positively stained immunohistochemically with antibody against amyloid beta-protein (A beta P) 1-40 synthetic peptide, but all diffuse and some primitive plaques were negative for antibody against A beta P 8-17 synthetic peptide. Neither senile plaque nor amyloid angiopathy was detected in the cerebrum of 15 young monkeys, 9 to 11 years old, examined as controls.
An RS-170 Camera For The Military Environment (1989)

This paper describes a new RS-170 video camera for use in the military environment. The camera is designed so that it can be reconfigured for various defense applications. A functional description of the detector, an area array Charge Coupled Device (CCD), and the video processing circuitry is provided. The camera&apos;s Signal-to-Noise Ratio (SNR) and various other important performance parameters are discussed.
Prevalence and clinical significance of incidental paraprosthetic valvar regurgitation: a prospective study using transoesophageal echocardiography (2003)

Small paraprosthetic leaks are common, are related to surgical factors, are not associated with increased subclinical haemolysis, and are benign during the first year after heart valve replacement.
Toward Gene Therapy for Niemann-Pick Disease (NPD): Separation of Retrovirally Corrected and Noncorrected NPD Fibroblasts Using a Novel Fluorescent Sphingomyelin (1992)

The neurologic (type A) and nonneurologic (type B) forms of Niemann-Pick disease (NPD) both result from deficiencies of acid sphingomyelinase (ASM) activity leading to the accumulation of sphingomyelin and other related lipids within lysosomes. Recently, the full-length cDNA and genomic sequences encoding ASM have been isolated and the nature of the molecular lesions causing NPD has been investigated. Although these developments have facilitated diagnosis for this debilitating disease, no effective treatment is currently available. Toward this latter goal, our laboratories recently reported the effectiveness of retroviral-mediated gene transfer for the in vitro correction of the cellular pathology in NPD fibroblasts (Suchi et al., 1992). In addition, novel selection procedures were developed to separate retrovirally corrected and noncorrected NPD fibroblasts based on the receptor-mediated delivery of a fluorescently (pyrene)-labeled sphingomyelin (P12-SPM) to the lysosomes of cells using liposomes coated with apolipoprotein E. In this study, we have used a different, fluorescent derivative of sphingomyelin (lissamine-rhodamine dodecanoyl sphingomyelin; LR12-SPM) to extend and improve this selection system. LR12-SPM offers a number of advantages over P12-SPM, including the facts that apolipoprotein E is not required for its efficient uptake and targeting to lysosomes and that the product of LR12-SPM degradation by ASM is efficiently transported out of cells. Thus, when analyzed in a fluorescence-activated cell sorter (FACS), there was complete separation (i.e., no overlap) of retrovirally corrected and noncorrected NPD cells after the administration of LR12-SPM.(ABSTRACT TRUNCATED AT 250 WORDS)
Cancer Prognosis Prediction Using Balanced Stratified Sampling (2014)

High accuracy in cancer prediction is important to improve the quality of the treatment and to improve the rate of survivability of patients. As the data volume is increasing rapidly in the healthcare research, the analytical challenge exists in double. The use of effective sampling technique in classification algorithms always yields good prediction accuracy. The SEER public use cancer database provides various prominent class labels for prognosis prediction. The main objective of this paper is to find the effect of sampling techniques in classifying the prognosis variable and propose an ideal sampling method based on the outcome of the experimentation. In the first phase of this work the traditional random sampling and stratified sampling techniques have been used. At the next level the balanced stratified sampling with variations as per the choice of the prognosis class labels have been tested. Much of the initial time has been focused on performing the pre-processing of the SEER data set. The classification model for experimentation has been built using the breast cancer, respiratory cancer and mixed cancer data sets with three traditional classifiers namely Decision Tree, Nave Bayes and K-Nearest Neighbour. The three prognosis factors survival, stage and metastasis have been used as class labels for experimental comparisons. The results shows a steady increase in the prediction accuracy of balanced stratified model as the sample size increases, but the traditional approach fluctuates before the optimum results.
Effect of Dead-Time on the Estimation of the Two-Sample Variance (1979)

Expressions for the averaged two-sample variance as well as expressions for the uncertainty on its estimation are given, in cases where dead time is present between measurements. The effect of this dead time on the precision of the time domain measure of frequency stability, in the presence of a limited number of data, is specified. The possibility to distinguish between white and flicker noises is pointed out.
Developments in Computer-Controlled Television Switchers (1973)

Four new presentation control rooms have been built in Edmonton and Toronto utilizing the experience gained from recent automated installations. A standard layout and computer system is used in each. The data entry is from magnetic data cassettes rather than from punched cards used previously. Standard business-type cathode-ray-tube terminals are used to prepare and utilize the cassettes, giving an easy compatibility with administrative computers used off-line to process program data.
Isolation, characterization, and analysis of the expression of the cbhII gene of Phanerochaete chrysosporium (1994)

Two cDNA sequences representing putative allelic variants of the Phanerochaete chrysosporium cbhII gene were isolated by hybridization to the Trichoderma reesei cbhII gene. Both of the equivalent genomic sequences were subsequently isolated by the inverse PCR technique. DNA sequencing showed that the cbhII open reading frame of 1,380 bp codes for a putative polypeptide of 460 amino acids which is interrupted by six introns. The domain structure found in T. reesei cbhII is conserved in the equivalent P. chrysosporium protein. The overall similarity between the two gene products is 54%, with the region of highest conservation being found in the cellulose-binding domain (65%). Unlike the cbhI gene of P. chrysosporium, cbhII does not appear to be a member of a class of closely related genes. CBHII is a new member of family B of the beta-1, 4-glucanases. Alignment of the P. chrysosporium and T. reesei CBHII protein sequences showed that all of the residues important for the formation of the extended loops of the catalytic domain and those residues that are involved in the catalytic action of the T. reesei enzyme are also present in the P. chrysosporium equivalent. The profiles of cbh gene expression in P. chrysosporium reveal that while cbhI.1 and cbhI.2 could be coregulated, cbhII can be independently controlled. The latter is so far the only cellulase gene found to be expressed when the fungus is grown on oat spelt arabinoxylan, suggesting that it may play an active role in the xylanolytic as well as the cellulolytic systems.
Can the Monomer of the Leucine Zipper Proteins Recognize the Dimer Binding Site without Dimerization? (1996)

It is generally believed that leucine zipper regulatory proteins for DNA transcription recognize their DNA binding sites as dimers preformed in solution (and that the monomers do not bind specifically to these sites). To test this idea, we synthesized the 31-residue peptide v-Jun-br, which contains only the DNA binding region of the v-Jun monomer. Footprinting assays show that v-Jun-br monomers specifically protect the DNA binding site of v-Jun in almost identically the same way as dimers. Thus, (i) the monomer recognizes the half-site of the dimer binding site and (ii) dimerization does not appreciably affect the bound conformation of each monomer. These results may have implications in the regulation of transcription by such proteins. Thus, two monomers of v-Jun might bind sequentially to the dimer binding site followed by dimerization of v-Jun while bound. This may allow binding at concentrations too low for dimerization in solution.
A robust method for isotopic riboprobe in situ hybridisation to localise mRNAs in routine pathology specimens. (1998)

In situ Hybridisation (ISH) to detect mRNA is widely applicable to studies of human pathology and experimental models including transgenic mice, where it can provide crucial information as to where a gene is expressed, that is not available in other ways. ISH was used to establish that relatively high levels of expression of E-cadherin mRNA were associated with long-term survival in colorectal cancer, before suitable antisera became available. There is increasing awareness that ISH can be used to help select between candidate disease genes found at a linked locus, and that ISH can help validate therapeutic targets. For instance, when several closely related receptor genes are expressed in a tissue, it may be possible to determine which combinations are expressed together in a single cell type. These diverse applications demand a robust method that works on a variety of clinical and experimental materials, and is easily interpreted. To date, the ICRF in situ Hybridisation Service has hybridised over 30,000 sections of principally formalin-fixed, paraffin-embedded tissues, with a high success rate. The practicalities of our preferred method are discussed and key steps for quality control highlighted.