gebhart/patrepeval huggingface dataset:
Expression of class II antigens by subsets of activated T cells (1986)

Gene products coded for within the HLA complex play an important role in the control of immune responses. Class I antigens, coded for by the HLA-A, B, and C loci, are expressed by virtually all mononuclear blood cells. Class II antigens, coded for by the DR, DQ, and DP loci, have a more limited tissue distribution. They are expressed by B cells, monocytes, and by activated, but not by resting, T cells. The class II molecules of B cells and antigen-presenting cells have long been of interest to immunologists, since they are involved in the presentation of antigen, in communication between T cells and B cells and between T cells and adherent cells, and in susceptibility to certain diseases. The class II antigens expressed by activated T cells, however, remain largely uncharacterized in terms of their specificity, functional significance, and molecular nature. We have studied the expression of DR and DQ antigens by activated T cells and then examined the expression of DR versus DQ antigens by Leu 2a and Leu 3a subsets of mitogen-activated populations. Our results demonstrated that, as for class II-positive macrophages, the intensity of staining with monoclonal antibodies directed against DR antigens was much greater than that obtained with those directed against DQ antigens. Interestingly, the percentages of Leu 2a- and Leu 3a-positive cells which expressed DR antigens were quite similar, as were the percentages of Leu 2a and Leu 3a cells which expressed DQ. Thus, there does not seem to be preferential expression of DR versus DQ antigens by mitogen-activated T-cell subsets. Finally, though both DR-positive-DQ-positive and DR-positive-DQ-negative populations were detected, few or no DR-negative-DQ-positive cells were observed in these populations.
A Mutation of the Circadian System in Golden Hamsters (1988)

A mutation has been found that dramatically shortens the period of the circadian locomotor rhythm of golden hamsters. The pattern of inheritance of this mutation suggests that it occurred at a single, autosomal locus ( tau ). Wild-type animals have rhythms with free-running periods averaging about 24 hours; animals heterozygous for the mutation have periods of about 22 hours, whereas homozygous animals have rhythms with periods close to 20 hours. Animals that carry the mutant alleles exhibit abnormal entrainment to 24-hour light:dark cycles or are unable to entrain.
Comparison of Selection Strategies for Marker‐Assisted Backcrossing of a Gene (1999)

Marker‐assisted selection can accelerate recovery of the recurrent parent genome (RPG) in backcross breeding. In this study, we used computer simulations to compare selection strategies with regard to (i) the proportion of the RPG recovered and (ii) the number of marker data points (MDP) required in a backcross program designed for introgression of one target allele from a donor line into a recipient line. Simulations were performed with a published maize ( Zea mays L.) genetic map consisting of 80 markers. Selection for the target allele was based on phenotypic evaluation. In comparison to a constant population size across all generations, increasing population sizes from generation BC 1 to BC 3 reduced the number of required MDP by as much as 50% without affecting the proportion of the RPG. A four‐stage selection approach, emphasizing in the first generations selection for recombinants on the carrier chromosome of the target allele, reduced the required number of MDP by as much as 75% in comparison to a selection index taking into account all markers across the genome. Adopting the above principles for the design of marker‐assisted backcross programs resulted in substantial savings in the number of MDP required.
An efficient newton‐like method for molecular mechanics energy minimization of large molecules (1987)

Abstract Techniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O ( N 2 )) and computer time of O ( N 3 ). Our suggested implementation of the Truncated Newton technique requires storage of less than O ( N 1.5 ) and CPU time of less than O ( N 2 ) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10 −6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
Tobacco genes expressed during in vitro floral initiation and their expression during normal plant development. (1989)

Since the transition from vegetative to floral development in plants is likely to be influenced by gene expression in several plant organs, we have used an in vitro system, the tobacco "thin cell layer" system as a model for investigating gene expression associated with the initiation of flowering in higher plants. cDNA cloning has been used to identify mRNAs abundant during thin cell layer floral initiation. These genes are expressed in thin cell layer explants initiating floral meristems but not in thin cell layer explants initiating vegetative shoot meristems or possessing roots. Two of these genes are expressed transcriptionally in incipient floral apices during normal plant development. Transcripts of these genes, plus a third gene, occur at low levels in several plant organs and at high levels in the roots, with the maximum levels of root expression reached just prior to the formation of floral meristems.
Microwave-Assisted Synthesis of Salicylamide via BCl3 Mediated Coupling (2005)

A novel and efficient microwave-assisted, BCl3-mediated coupling reaction to synthesize salicylamide structures from phenols and isocyanates is described.
Gene silencing using micro-RNA designed hairpins (2002)

During RNA interference (RNAi), long dsRNA is processed to approximately 21 nt duplexes, short interfering RNAs (siRNAs), which silence genes through a mRNA degradation pathway. Small temporal RNAs (stRNAs) and micro-RNAs (miRNAs) are approximately 21 nt RNAs that are processed from endogenously encoded hairpin-structured precursors, and function to silence genes via translational repression. Here we report that synthetic hairpin RNAs that mimic siRNAs and miRNA precursor molecules can target a gene for silencing, and the mechanism of silencing appears to be through mRNA degradation and not translational repression. The sequence and structural configuration of these RNAs are important, and even slight modification in structure can affect the silencing activity of the hairpins. Furthermore, these RNAs are active when expressed by DNA vectors containing polymerase III promoters, opening the possibility for new approaches in stable RNAi-based loss of function studies.
Extracellular Matrix Regulation of Stem Cell Behavior (2016)

Stem cells hold great promise in treating many diseases either through promoting endogenous cell repair or through direct cell transplants. In order to maximize their potential, understanding the fundamental signals and mechanisms that regulate their behavior is essential. The extracellular matrix (ECM) is one such component involved in mediating stem cell fate. Recent studies have made significant progress in understanding stem cell-ECM interactions. Technological developments have provided greater clarity in how cells may sense and respond to the ECM, in particular the physical properties of the matrix. This review summarizes recent developments, providing illustrative examples of the different modes with which the ECM controls both embryonic and adult stem cell behavior.
Continuous separation of particles in a PDMS microfluidic channel via travelling surface acoustic waves (TSAW) (2013)

We demonstrate a simple and efficient device for the continuous label-free separation of microparticles using travelling surface acoustic waves (TSAW). A focusing interdigitated unidirectional transducer released high frequency (133.3 MHz) TSAW normal to the fluid flow direction to segregate 3 μm particles from 10 μm particles with a separation efficiency of 100%. The TSAW based separator does not necessitate a tight alignment of the PDMS microchannel with the transducer.
Performance evaluation of a multiplex assay for future use in biomarker discovery efforts to predict body composition (2011)

Serum and plasma performed similarly for the majority of the analytes. Serum showed a slight advantage in predicting extreme body composition phenotypes in postmenopausal women using parallel evaluation of analytes.
Sources of DNA for detecting B cell monoclonality using PCR. (1994)

PCR determination of B cell clonality using paraffin wax embedded material is sufficiently sensitive and reliable for use as a routine diagnostic adjunct to conventional morphological and immunocytochemical assessment of lymphoproliferative disease.
Efficient gene targeting in Kluyveromyces lactis (2004)

Integration of a DNA fragment in a host genome requires the action of a double-strand break (DSB) repair mechanism. Homologous recombination (HR) is initiated by binding of Rad52p to DNA ends and results in targeted integration. Binding of the Ku heterodimer (Ku70p/Ku80p) results in random integration via non-homologous end joining (NHEJ). In contrast to Saccharomyces cerevisiae, the budding yeast Kluyveromyces lactis shows variable, but in general low, gene targeting efficiency. To study and to improve gene targeting efficiency, K. lactis has been used as a model. The KlRAD51, KlRAD52 and KlKU80 genes have been isolated and deletion mutants for these genes have been constructed. Efficiency of gene targeting was determined at the KlADE2 locus using targeting constructs with different lengths of homologous flanking sequences. In wild-type K. lactis, the gene targeting efficiency ranged from 0% with 50 to 88% with 600 bp flanks. The Klku80 mutant, however, showed >97% gene targeting efficiency independently of the size of the homologous flanks. These results demonstrate that deletion of the NHEJ mechanism results in a higher gene targeting efficiency. Furthermore, increased gene targeting efficiency was achieved by the transformation of wild-type K. lactis with the KlADE2 deletion construct in the presence of excess small DNA fragments. Using this method, PCR-generated deletion constructs containing only 50 bp of homologous flanking sequences resulted in efficient targeted gene replacement.
Adverse drug events in hospitalized patients. Excess length of stay, extra costs, and attributable mortality. (1997)

The attributable lengths of stay and costs of hospitalization for ADEs are substantial. An ADE is associated with a significantly prolonged length of stay, increased economic burden, and an almost 2-fold increased risk of death.
Enhanced Glycolytic Metabolism Contributes to Cardiac Dysfunction in Polymicrobial Sepsis (2017)

Glycolytic metabolism plays an important role in mediating sepsis-induced septic cardiomyopathy. The mechanisms may involve regulation of inflammatory response and apoptotic signaling.
Drug Inducible CRISPR/Cas Systems (2019)

Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have been employed as a powerful versatile technology for programmable gene editing, transcriptional modulation, epigenetic modulation, and genome labeling, <i>etc.</i> Yet better control of their activity is important to accomplish greater precision and to reduce undesired outcomes such as off-target events. The use of small molecules to control CRISPR/Cas activity represents a promising direction. Here, we provide an updated review on multiple drug inducible CRISPR/Cas systems and discuss their distinct properties. We arbitrarily divided the emerging drug inducible CRISPR/Cas systems into two categories based on whether at transcription or protein level does chemical control occurs. The first category includes Tet-On/Off system and Cre-dependent system. The second category includes chemically induced proximity systems, intein splicing system, 4-Hydroxytamoxifen-Estrogen Receptor based nuclear localization systems, allosterically regulated Cas9 system, and destabilizing domain mediated protein degradation systems. Finally, the advantages and limitations of each system were summarized.
Timing of SV40 oncogene activation by site-specific recombination determines subsequent tumor progression during murine lens development. (1993)

We generated mice that carry copies of a dormant transgene encoding the SV40 tumor antigens. The transgenes are specifically targeted to the lens and contain features that render their expression dependent on the action of Cre, a site-specific bacteriophage DNA recombinase. Timing of oncogene activation was controlled by making Cre available either prior to, or coincident with, the onset of primary fiber differentiation in the embryonic lens vesicle. Early expression of Cre resulted in oncogene activation in undifferentiated lens epithelial cells that rapidly proliferated inside the lens capsule. By contrast, when Cre accumulation was delayed to coincide with the onset of primary lens fiber differentiation, SV40 oncogenes were activated in cells that had begun to elongate and to accumulate lens-specific crystallins. During subsequent proliferation inside the lens capsule, transformed progeny cells maintained the profile of fiber differentiation that their parent cells had acquired at the time of oncogenic conversion. Developing lens tumors were confined within the capsule of the embryonic lens. However, if the capsule was perforated in an embryonic eye in organ culture, cells rapidly grew out while still maintaining features of differentiation. Our findings show that the differentiated state of the primary target cells is an important parameter of subsequent lens oncogenesis, and that an intact lens capsule can restrict invasive neoplastic growth.
Charles Babbage - computer pioneer (1991)

Abstract 1991 is the bicentenary of the birth of Charles Babbage[1], the great pioneer of digital computing. The event is being celebrated by a postage stamp, many small exhibitions, a major conference on computing organised by the IEE to be held at Imperial College in July, and a full-sized working version of Babbage's second difference engine now being assembled at the Science Museum.
Progress and perspectives on halide lithium conductors for all-solid-state lithium batteries (2020)

This review focuses on fundamental understanding, various synthesis routes, chemical/electrochemical stability of halide-based lithium superionic conductors, and their potential applications in energy storage as well as related challenges.
A Recurrent Neural Network for Solving Nonlinear Convex Programs Subject to Linear Constraints (2005)

In this paper, we propose a recurrent neural network for solving nonlinear convex programming problems with linear constraints. The proposed neural network has a simpler structure and a lower complexity for implementation than the existing neural networks for solving such problems. It is shown here that the proposed neural network is stable in the sense of Lyapunov and globally convergent to an optimal solution within a finite time under the condition that the objective function is strictly convex. Compared with the existing convergence results, the present results do not require Lipschitz continuity condition on the objective function. Finally, examples are provided to show the applicability of the proposed neural network.
Lengths of chromosomal segments conserved since divergence of man and mouse. (1984)

Linkage relationships of homologous loci in man and mouse were used to estimate the mean length of autosomal segments conserved during evolution. Comparison of the locations of greater than 83 homologous loci revealed 13 conserved segments. Map distances between the outermost markers of these 13 segments are known for the mouse and range from 1 to 24 centimorgans. Methods were developed for using this sample of conserved segments to estimate the mean length of all conserved autosomal segments in the genome. This mean length was estimated to be 8.1 +/- 1.6 centimorgans. Evidence is presented suggesting that chromosomal rearrangements that determine the lengths of these segments are randomly distributed within the genome. The estimated mean length of conserved segments was used to predict the probability that certain loci, such as peptidase-3 and renin, are linked in man given that homologous loci are chi centimorgans apart in the mouse. The mean length of conserved segments was also used to estimate the number of chromosomal rearrangements that have disrupted linkage since divergence of man and mouse. This estimate was shown to be 178 +/- 39 rearrangements.
Random Filters for Compressive Sampling and Reconstruction (2006)

We propose and study a new technique for efficiently acquiring and reconstructing signals based on convolution with a fixed FIR filter having random taps. The method is designed for sparse and compressible signals, i.e., ones that are well approximated by a short linear combination of vectors from an orthonormal basis. Signal reconstruction involves a nonlinear orthogonal matching pursuit algorithm that we implement efficiently by exploiting the nonadaptive, time-invariant structure of the measurement process. While simpler and more efficient than other random acquisition techniques like compressed sensing, random filtering is sufficiently generic to summarize many types of compressible signals and generalizes to streaming and continuous-time signals. Extensive numerical experiments demonstrate its efficacy for acquiring and reconstructing signals sparse in the time, frequency, and wavelet domains, as well as piecewise smooth signals and Poisson processes
TEAM-MANAGED HOME-BASED PRIMARY CARE IN SINGAPORE: A CASE SERIES THAT DEMONSTRATES COST SAVING (2017)

Home-based care is commonly perceived as costly and limited in reach. This paper investigates cost savings (or the lack of it) generated from a Singapore-based medical home-care called ‘Hua Mei Mobile Clinic’ (HMMC), which has been in operation since 1993. HMMC is an initiative from Tsao Foundation, an non-governmental organization that has a vision for assisting the elders ‘to be a master of one’s destiny and ‘to have meaning in life even when one is near the end of it’. Elders recruited to HMMC are generally of advanced age, having multiple comorbidities and needing intensive health and social interventions. The core features of HMMC are: Primary Care Approach; Comprehensive Needs Assessment; Interdisciplinary Team care processes; Regular Team Communication; and 24/7 Access. Method: Pre- and post-HMMC enrolment health utilization data were studied for elders who fulfilled the following the criteria: 1) enrolled to HMMC from 1st January 2013 to 31st December 2015 for six months or more; 2) health utilization data were accessible from HMMC electronic medical records. Pre- and post-enrolment data were then compared. Results: 62 elders were included in the study. There was a reduction in Emergency Department attendance by 62%; reduction in acute hospital admissions by 54%; as well as reduction in length of hospital stay 83%. Conclusion: HMMC had demonstrated cost savings in terms of the reduction in the use of tertiary heath care resources. This study would be developed into a cost-benefit analysis to compare such cost saving with the cost of operating HMMC.
Myristylation of gag protein in human T-cell leukemia virus type-I and type-II. (1985)

We found that p19gag of HTLV-I and p23gag of HTLV-II are myristylated. The p28, which is immunologically cross-reactive with monoclonal antibody against p19gag of HTLV-I was also shown to be myristylated in the HTLV-I-infected cell lines MT-2 and HUT102. However, no myristylated p28 was found in HTLV-II-infected cell lines, Mo and Ton1.
Ultrasound imaging software framework for real-time monitoring of acoustic ablation therapy (2012)

The concern with interstitial ablative therapy for a treatment of hepatic tumors has been growing. In spite of advances in these therapies, there are several technical challenges due to tissue deformation and target motion: localization of the tumor and monitoring for ablator's tip and thermal dose in heated tissue. In the previous work, a steerable acoustic ablator, called ACUSITT, for targeting of ablation tip accurately into tumor area has been developed. However, real-time monitoring techniques for providing image feedback of the ablation tip positioning and thermal dose deposited in the tissue by heating are still needed. In this paper, a new software framework for real-time monitoring ablative therapy during pre- and intra-operation is presented. The software framework provides ultrasound Brightness Mode (B-Mode) image and elastography simultaneously and with real-time. A position of ablator's tip and a region of heated tissue are monitored on B-Mode image, because the image represents tissue morphology. Furthermore, ultrasound elasticity image is used for finding a boundary and region of tumor on pre-ablation, and monitoring thermal dose in tissue during ablation. By providing B-Mode image and elastography at the same time, reliable information for monitoring thermal therapy can be offered.
Surgery by Laser for Malignant Melanoma (1979)

Lasers have been used for photocoagulation and photoexcision of malignant melanomas when conventional instruments could not be used. Lasers are useful for destruction of cutaneous metastases from malignant melanomas especially when numerous and dispersed. The color of melanomas makes for selective absorption of energy from lasers in the visible light range. Surgery by lasers is still an investigative form of surgery with current research studies on immediate placement of grafts, lymphatic migration of malignant cells after laser surgery, and relevant immunologic studies.
Neutralizing Antibodies Directed Against Osteopontin Inhibit Rat Carotid Neointimal Thickening After Endothelial Denudation (1997)

Osteopontin is an arginine-glycine-aspartate-containing acidic glycoprotein with adhesive and migratory activities in vitro. We previously showed that osteopontin was highly expressed in injured rat arteries as well as in human atherosclerotic plaques. In contrast, uninjured blood vessels make very little osteopontin. In this report, we have investigated the role of osteopontin in rat neointima formation using neutralizing antibodies. Rats were treated with either nonimmune or antiosteopontin antibody and subjected to endothelial denudation of the carotid artery by using a balloon catheter. Two weeks after injury, intimal areas and cell numbers were significantly decreased (33% and 31%, respectively) in the antiosteopontin group compared with the nonimmune IgG group. No differences in carotid medial areas or cell numbers were observed. Intimal and medial replication rates, as measured by continuous bromodeoxyuridine infusion during the final week of the experimental protocol, were not significantly different between the two groups. No gross histological changes were noted in the intimas formed in the presence of either neutralizing or nonimmune antibody. In addition, no difference in early carotid medial cell replication rate was observed when antibodies were infused for 4 days after angioplasty. These data demonstrate for the first time a functional role for osteopontin in the process of carotid neointimal thickening in vivo and suggest that osteopontin plays an active role in the remodeling processes important for human atherosclerotic and restenotic lesion development.