gebhart/patrepeval huggingface dataset:
Optimal scheduling of transient cycles for single-armed cluster tools (2013)

Cluster tools, widely used for wafer fabrication processes, have complex scheduling problems because a tool consists of several single-wafer processing chambers and a robot, and has a number of scheduling constraints. Most scheduling studies on cluster tools have focused on steady cyclic cycles where identical work cycles are repeated. However, as the lot size tends to be smaller, a tool has longer noncyclic operation cycles such as the start-up and the close-down. Therefore, we examine a way of scheduling for noncyclic cycles of single-armed cluster tools so as to minimize the makespan. To do this, we first analyse fundamental properties of tool behaviours including noncyclic transient cycles. Using the properties, we identify the workload of processing a lot with a number of wafers. Then, we develop the condition for which the conventional backward sequence, which is known to be optimal for cyclic work cycles, has the optimal makespan. Finally, we develop a linear programming model to find the minimum makespan of the backward sequence.
Receptor Ligand-Facilitated Gene Transfer: Enhancement of Liposome-Mediated Gene Transfer and Expression by Transferrin (1996)

A high-efficiency, nonviral gene transfer protocol employing cationic liposome plus a receptor ligand is described. The delivery of the beta-galactosidase (beta-Gal) gene (pCMVlacZ) by lipofectin plus transferrin can achieve 98-100% transfection of HeLa cells as compared to 3-4% by lipofectin alone. A dose-dependent gene transfer was observed between 1 and 16 micrograms transferrin, and maximal transfection efficiency was obtained at > or = 16 micrograms transferrin. The expression of beta-Gal activity in 100% transfected cells decreased progressively with each passage and returned to the baseline value after six passages, indicating that the DNA delivered was only transiently expressed. The amount of DNA delivered to the cells by lipofectin plus transferrin was approximately two times that obtained by lipofectin, which in turn was two times that by transferrin or without lipofectin and transferrin. In addition, DNA can form complexes with lipofectin and transferrin. These results suggest that transferrin enhances gene transfer and expression in the presence of lipofectin by further facilitating the entry of DNA into the cells through the lipofectin-DNA-transferrin complex. The enhancement of liposome-mediated gene transfer efficiency and expression by transferrin varies with different cationic liposomes. The four different liposomes examined show the following relative transfection efficiency: transfectin > lipofectACE > > DC-cholesterol > > lipofectAMINE.
Sciatic nerve regeneration in rats induced by transplantation of in vitro differentiated bone‐marrow stromal cells (2001)

Bone marrow stromal cells (MSCs) are multipotent stem cells that have the potential to differentiate into bone, cartilage, fat and muscle. We now demonstrate that MSCs can be induced to differentiate into cells with Schwann cell characteristics, capable of eliciting peripheral nervous system regeneration in adult rats. MSCs treated with beta-mercaptoethanol followed by retinoic acid and cultured in the presence of forskolin, basic-FGF, PDGF and heregulin, changed morphologically into cells resembling primary cultured Schwann cells and expressing p75, S-100, GFAP and O4. The MSCs were genetically engineered by transduction with retrovirus encoding green fluorescent protein (GFP), and then differentiated by treatment with factors described above. They were transplanted into the cut ends of sciatic nerves, which then responded with vigorous nerve fibre regeneration within 3 weeks of the operation. Myelination of regenerated fibers by GFP-expressing MSCs was recognized using confocal and immunoelectron microscopy. The results suggest that MSCs are able to differentiate into myelinating cells, capable of supporting nerve fibre re-growth, and they can therefore be applied to induce nerve regeneration.
Purification and partial characterization of another form of the antiviral protein from the seeds of Phytolacca americana L. (pokeweed) (1982)

1. The pokeweed antiviral protein, previously identified in two forms (PAP and PAP II) in the leaves of Phytolacca americana (pokeweed) [Obrig. Irvin & Hardesty (1973) Arch. Biochem. Biophys. 155, 278-289; Irvin, Kelly & Robertus (1980) Arch. Biochem. Biophys. 200, 418-425] is a protein that prevents replication of several viruses and inactivates ribosomes, thus inhibiting protein synthesis. 2. PAP is present in several forms in the seeds of pokeweed. One of them, which we propose to call 'pokeweed antiviral protein from seeds' (PAP-S) was purified in high yield (180 mg per 100 g of seeds) by chromatography on CM-cellulose, has mol.wt. 30 000, and is similar to, but not identical with. PAP and PAP II. 3. PAP-S inhibits protein synthesis in a rabbit reticulocyte lysate with an ID50 (concentration giving 50% inhibition) of 1.1 ng/ml (3.6 x 10(-11) M), but has much less effect on protein synthesis by whole cells, with an ID50 of 1 mg/ml (3.3 x 10(-5) M), and inhibits replication of herpes simplex virus type 1.
Molecular Targeted Therapy in Prevalent Tumors: Learning from the Past and Future Perspectives (2010)

Important advances have been achieved with molecular targeted agents in clinical oncology. Breast, colon, and lung cancer, are now commonly treated with a combination of chemotherapy and targeted agents. In this article the authors discuss the limitations of targeted therapy development, failures of previous studies, and possible strategies for an intelligent drug development. Initial attempts to block mTOR in breast cancer, the magnitude of benefit obtained with anti-EGFR therapy in lung cancer, and the narrowing use of anti-EGFR therapy in colon cancer based on KRAS status are discussed.
Can C reactive protein or troponins T and I predict outcome in patients with intractable unstable angina? (1998)

In patients transferred to a tertiary centre with intractable chest pain, C reactive protein and troponin I are not predictive of transient myocardial ischaemia or lesion morphology, both of which are surrogate markers of outcome. Troponin T is, however, raised in patients with multivessel disease or transient myocardial ischaemia. These serum protein assays cannot be used to stratify the risk of patients with unstable angina who are awaiting transfer to the tertiary centre.
Clinical evaluation of a PHMBimpregnated biocellulose dressing on paediatric lacerations (2011)

None. The authors have no relevant financial interest in this article. All authors were involved in the critical revision of the manuscript for important intellectual content.
Heterogeneity of low density lipoprotein responses to fish-oil supplementation in hypertriglyceridemic subjects. (1989)

Previous studies have demonstrated a variable effect of fish oil on low density lipoprotein (LDL) cholesterol and apolipoprotein (apo) B levels, particularly in hypertriglyceridemic subjects. Since heterogeneity of LDL composition and metabolism in hypertriglyceridemic subjects is well described, the present study was undertaken to determine if the response of LDL to dietary fish-oil supplementation is dependent upon pretreatment differences in LDL composition. A single-blind, cross-over design was used with 18 hypertriglyceridemic subjects, who were given supplements of a safflower-oil placebo or a fish-oil concentrate (4.0 g omega-3 fatty acids; [F4 dose]) for 1 month. Sixteen subjects then received an additional month of fish-oil supplementation at a higher dose (7.5 g omega-3 fatty acids [F7.5 dose]). The initial LDL cholesterol/apo B ratio, an index of LDL composition, was correlated positively with changes in LDL apo B levels (F4.0 dose: r = 0.41, p = 0.06; F7.5 dose: r = 0.51, p = 0.03) and negatively with changes in LDL cholesterol concentrations (F4.0 dose: r = -0.51, p = 0.01; F7.5 dose: r = -0.50, p = 0.02). Twelve subjects with LDL cholesterol/apo B ratios above 1.4 had large increases in LDL apo B (51% at both doses, p less than 0.05) but much smaller changes in LDL cholesterol levels during fish-oil treatment. Six subjects with LDL cholesterol/apo B ratios below 1.4 showed a trend toward increased LDL cholesterol (12% increase from baseline at F4 dose, 10% increase from baseline at F7.5 dose, p greater than 0.05) but not in LDL apo B levels during fish-oil therapy. These data suggest that LDL responses to fish oil may be linked to underlying differences in LDL composition and, presumably, to differences in LDL metabolic behavior.
Action of RNase II and Polynucleotide Phosphorylase against RNAs Containing Stem-Loops of Defined Structure (2000)

The 3'-->5' exoribonucleases, RNase II and polynucleotide phosphorylase (PNPase), play an essential role in degrading fragments of mRNA generated by prior cleavages by endonucleases. We have assessed the ability of small RNA substrates containing defined stem-loop structures and variable 3' extensions to impede the exonucleolytic activity of these enzymes. We find that stem-loops containing five G-C base pairs do not block either enzyme; in contrast, more stable stem-loops of 7, 9, or 11 bp block the processive action of both enzymes. Under conditions where enzyme activity is limiting, both enzymes stall and dissociate from their substrates six to nine residues, on average, from the base of a stable stem-loop structure. Our data provide a clear mechanistic explanation for the previous observation that RNase II and PNPase behave as functionally redundant.
Closed-form solution of absolute orientation using orthonormal matrices (1988)

Finding the relationship between two coordinate systems by using pairs of measurements of the coordinates of a number of points in both systems is a classic photogrammetric task. The solution has applications in stereophotogrammetry and in robotics. We present here a closed-form solution to the least-squares problem for three or more points. Currently, various empirical, graphical, and numerical iterative methods are in use. Derivation of a closed-form solution can be simplified by using unit quaternions to represent rotation, as was shown in an earlier paper [ J. Opt. Soc. Am. A4, 629 ( 1987)]. Since orthonormal matrices are used more widely to represent rotation, we now present a solution in which 3 × 3 matrices are used. Our method requires the computation of the square root of a symmetric matrix. We compare the new result with that obtained by an alternative method in which orthonormality is not directly enforced. In this other method a best-fit linear transformation is found, and then the nearest orthonormal matrix is chosen for the rotation. We note that the best translational offset is the difference between the centroid of the coordinates in one system and the rotated and scaled centroid of the coordinates in the other system. The best scale is equal to the ratio of the root-mean-square deviations of the coordinates in the two systems from their respective centroids. These exact results are to be preferred to approximate methods based on measurements of a few selected points.
Revisiting the Role of Glycosylation in the Structure of Human IgG Fc (2012)

Binding of the Fc domain of Immunoglobulin G (IgG) to Fcγ receptors on leukocytes can initiate a series of signaling events resulting in antibody-dependent cell-mediated cytotoxicity (ADCC) and other important immune responses. Fc domains lacking glycosylation at N297 have greatly diminished Fcγ receptor binding and lack the ability to initiate a robust ADCC response. Earlier structural studies of Fc domains with either full length or truncated N297 glycans led to the proposal that these glycans can stabilize an "open" Fc conformation recognized by Fcγ receptors. We determined the structure of an E. coli expressed, aglycosylated human Fc domain at 3.1 Å resolution and observed significant disorder in the C'E loop, a region critical for Fcγ receptor binding, as well as a decrease in distance between the C(H)2 domains relative to glycosylated Fc structures. However, comparison of the aglycosylated human Fc structure with enzymatically deglycosylated Fc structures revealed large differences in the relative orientations and distances between C(H)2 domains. To provide a better appreciation of the physiologically relevant conformation of the Fc domain in solution, we determined Radii of Gyration (R(g)) by small-angle X-ray scattering (SAXS) and found that the aglycosylated Fc displays a larger R(g) than glycosylated Fc, suggesting a more open C(H)2 orientation under these conditions. Moreover, the R(g) of aglycosylated Fc was reduced by mutations at the C(H)2-C(H)3 interface (E382V/M428I), which confer highly selective binding to FcγRI and novel biological activities.
Fingolimod and CSF neurofilament light chain levels in relapsing-remitting multiple sclerosis (2015)

Our results suggest a beneficial effect of fingolimod on this marker of axonal injury and support the utility of NfL as a quantitative biomarker in multiple sclerosis.
Mucosal model of genital immunization in male rhesus macaques with a recombinant simian immunodeficiency virus p27 antigen (1994)

Human immunodeficiency virus (HIV) can be transmitted through infected seminal fluid or vaginal or rectal secretions during heterosexual or homosexual intercourse. To prevent mucosal transmission and spread to the regional lymph nodes, an effective vaccine may need to stimulate immune responses at the genitourinary mucosa. In this study, we have developed a mucosal model of genital immunization in male rhesus macaques, by topical urethral immunization with recombinant simian immunodeficiency virus p27gag, expressed as a hybrid Ty virus-like particle (Ty-VLP) and covalently linked to cholera toxin B subunit. This treatment was augmented by oral immunization with the same vaccine but with added killed cholera vibrios. Polymeric secretory immunoglobulin A (sIgA) and IgG antibodies to p27 were induced in urethral secretions, urine, and seminal fluid. This raises the possibility that the antibodies may function as a primary mucosal defense barrier against SIV (HIV) infection. The regional lymph nodes which constitute the genital-associated lymphoid tissue contained p27-specific CD4+ proliferative and helper T cells for antibody synthesis by B cells, which may function as a secondary immune barrier to infection. Blood and splenic lymphocytes also showed p27-sensitized CD4+ T cells and B cells in addition to serum IgG and IgA p27-specific antibodies; this constitutes a third level of immunity against dissemination of the virus. A comparison of genito-oral with recto-oral and intramuscular routes of immunization suggests that only genito-oral immunization elicits specific sIgA and IgG antibodies in the urine, urethra, and seminal fluid. Both genito-oral and recto-oral immunizations induced T-cell and B-cell immune responses in regional lymph nodes, with preferential IgA antibody synthesis. The mucosal route of immunization may prevent not only virus transmission through the genital mucosa but also dissemination and latency of the virus in the draining lymph nodes.
Biochemical and functional analysis of a 9-nt RNA sequence that affects translation efficiency in eukaryotic cells (2004)

We previously identified an internal ribosome entry site (IRES) within the 5' leader of the mRNA encoding the Gtx homeodomain protein and showed that shorter nonoverlapping segments of this 5' leader could enhance the translation of a second cistron in a dicistronic mRNA. One of these segments was 9 nt in length, and when multiple copies of this IRES module were linked together, IRES activity was greatly enhanced. To further expand the potential uses of these synthetic constructs and facilitate analyses of the mechanism by which they affect translation, we show here that an IRES containing five linked copies of the 9-nt sequence can also enhance translation in the 5' leader of a monocistronic mRNA. Moreover, a search for interactions of the IRES module with cellular factors revealed specific binding to 40S ribosomal subunits but not to other cellular components. Based on the results of earlier studies suggesting that this sequence could bind to a complementary segment of 18S rRNA, we tested various sequences for possible links between the length of the complementary match, their binding to ribosomes, and their influence on translational efficiency. We found that the length of the complementary match was directly correlated with the ability of RNA probes to bind to ribosomes. In addition, translation was maximally enhanced ( approximately 8-fold) by a 7-nt segment of the 9-nt element; the enhancement declined progressively as the complementary stretches became progressively longer or shorter. The results suggest that the Gtx 9-nt sequence affects translation efficiency by a mechanism that involves base pairing to 18S rRNA.
CA IX is an Independent Prognostic Marker in Premenopausal Breast Cancer Patients with One to Three Positive Lymph Nodes and a Putative Marker of Radiation Resistance (2006)

CA IX is marker of poor prognosis in premenopausal breast cancer patients and it is an independent predictor of survival in patients with one to three positive lymph nodes. As all these patients received locoregional radiation therapy, CA IX may be associated with resistance to radiotherapy.
Preliminary experiments in robot/human cooperative microinjection (2004)

This paper reports preliminary experiments with a cooperative robot system to augment single cell manipulation tasks. The JHU "Steady-Hand" robot configuration for cell manipulation is reported. Stable force control laws for the "Steady Hand" are revisited. Preliminary experiments validating stable insertion of a micropipette in a mouse embryo are detailed along with formulation of vision based tracking and augmentation. These preliminary experiments demonstrate promise of cooperative augmentation in single cell manipulation tasks.
Spinal analgesic actions of the new endogenous opioid peptides endomorphin-1 and -2 (1997)

Two highly-selective mu-opioid receptor agonists, endomorphin-1 and -2, were recently purified from bovine brain and are postulated to be endogenous mu-opioid receptor ligands. We sought to determine the effects of these ligands at the spinal level in mice. Endomorphin-1 and -2 produced short acting, naloxone-sensitive antinociception in the tail flick test and inhibited the behavior elicited by intrathecally injected substance P. Both endomorphin-1 and -2 were anti-allodynic in the dynorphin-induced allodynia model. Although acute tolerance against both endomorphins developed rapidly, endomorphin-1 required a longer pretreatment time before tolerance was observed. We conclude that the endomorphins are potent spinal antinociceptive and anti-allodynic agents and that they or related compounds may prove therapeutically useful as spinal analgesics.
Ruthenium(ii) complexes of pyridinol and N-heterocyclic carbene derived pincers as robust catalysts for selective carbon dioxide reduction (2017)

A new pincer ligand with N-heterocyclic carbene (NHC) and 4-pyridinol-derived rings supports ruthenium complexes for photocatalytic CO<sub>2</sub> reduction. The methoxy group on the pyridine ring offers unique catalysis advantages not seen with the unsubstituted analog. Our best catalyst offers selective CO formation, ∼250 turnover cycles, and a 40 h lifetime.
Boron Nitride Composites By Chemical Vapor Deposition (1975)

Composites of boron nitride ( BN) have been made by the chemical vapor deposition ( CVD) of a BN matrix on a BN felt fiber substrate. Reactant gases were boron trifluoride and ammonia. The composites have a relatively high density (1.70 g/cm 3 ), a crystallite size L C = 150 A and an interlayer spacing d 002 = 3.35 A. Measurements of elastic modulus and thermal conductivity and expansion showed some anisotropy as a result of the preferred fiber orientation of the substrate.
Subgingival Bacteria - Comparison of Culture Results in Dogs and Cats with Gingivitis (1995)

Aerobic and anaerobic subgingival bacteria were cultured and identified from 49 dogs and 40 cats with spontaneous gingivitis. The most common organisms were gram-negative anaerobes (37% of canine isolates and 39% of feline isolates) and gram-positive aerobes (36% of canine isolates and 29% of feline isolates). No major differences were found between the subgingival floras of dogs and cats with gingivitis.
Potassium Trifluoro(organo)borates: New Perspectives in Organic Chemistry (2003)

Abstract Potassium trifluoro(organo)borates, highly stable organoboron derivatives, have recently emerged as promising alternatives to other organoboron reagents. These salts have shown interesting reactivity, not only through the intermediate formation of difluoroboranes, but also in transmetallation reactions with transition metals. In numerous reactions they have proven to be more reactive than boronic acids or esters. The preparation and reactivity of these ate complexes is discussed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Making the V in VQA Matter: Elevating the Role of Image Understanding in Visual Question Answering (2017)

Problems at the intersection of vision and language are of significant importance both as challenging research questions and for the rich set of applications they enable. However, inherent structure in our world and bias in our language tend to be a simpler signal for learning than visual modalities, resulting in models that ignore visual information, leading to an inflated sense of their capability. We propose to counter these language priors for the task of Visual Question Answering (VQA) and make vision (the V in VQA) matter! Specifically, we balance the popular VQA dataset (Antol et al., ICCV 2015) by collecting complementary images such that every question in our balanced dataset is associated with not just a single image, but rather a pair of similar images that result in two different answers to the question. Our dataset is by construction more balanced than the original VQA dataset and has approximately twice the number of image-question pairs. Our complete balanced dataset is publicly available at http://visualqa.org/ as part of the 2nd iteration of the Visual Question Answering Dataset and Challenge (VQA v2.0). We further benchmark a number of state-of-art VQA models on our balanced dataset. All models perform significantly worse on our balanced dataset, suggesting that these models have indeed learned to exploit language priors. This finding provides the first concrete empirical evidence for what seems to be a qualitative sense among practitioners. Finally, our data collection protocol for identifying complementary images enables us to develop a novel interpretable model, which in addition to providing an answer to the given (image, question) pair, also provides a counter-example based explanation. Specifically, it identifies an image that is similar to the original image, but it believes has a different answer to the same question. This can help in building trust for machines among their users.