gebhart/patrepeval huggingface dataset:
Tunable-Volume Handheld Pipette Utilizing a Pneumatic De-Amplification Mechanism (2014)

We present the design, analysis, and validation of a tunable-volume handheld pipette that enables precise drawing and dispensing of ml and μl liquid volumes. The design builds upon the standard mechanism of a handheld micropipette by incorporating an elastic diaphragm that de-amplifies the volume displacement of the internal piston via compression of an entrapped air volume. The degree of de-amplification is determined by the stiffness of the elastic diaphragm and the amount of entrapped air. An analytical model of the diaphragm mechanism is derived, which guides how to achieve linear de-amplification over an extended range where leading-order nonlinear contributions are significant. In particular, nonlinearities inherent in the mechanical behavior of the diaphragm and entrapped air volume may exactly cancel one another by careful design of the pipette’s parameter constants. This linearity is a key attribute for enabling the pipette’s tunable volumetric range, as this allows diaphragms with different stiffnesses to be selectively used with a conventional linear-stepping piston mechanism. Design considerations regarding the range, accuracy, and precision of the proposed pipette are detailed based on the model. Additionally, we have constructed a handheld prototype that uses a planar latex sheet as the diaphragm. Our pipetting experiments validate the derived model and exhibit linearity between the piston stroke and drawn liquid volume. We propose that this design enables a single handheld mechanical pipette to achieve drawing and dispensing of liquids over a 1μl-10ml range (i.e., the range of the entire micropipette suite), with volumetric resolution and precision comparable to commercially available counterparts.
Revision total knee arthroplasty for flexion instability (2022)

We found fair functional outcomes and implant survivorship at a mean of ten years after revision TKA for flexion instability with a PS implant. Recurrent instability and aseptic loosening were the most common indications for re-revision. Components with increased constraint, such as a VVC or hinged, should be used in these patients in order to reduce the risk of recurrent instability.Cite this article: <i>Bone Joint J</i> 2022;104-B(10):1126-1131.
An Improved Preparation of Trimethylarsine (1972)

Abstract As(CH3)3 is obtained in good yields from the normal Grignard procedure in ethyl ether, when isolated through its silver or copper nitrate complexes.
Programmed Death-1 Controls T Cell Survival by Regulating Oxidative Metabolism (2015)

The coinhibitory receptor programmed death-1 (PD-1) maintains immune homeostasis by negatively regulating T cell function and survival. Blockade of PD-1 increases the severity of graft-versus-host disease (GVHD), but the interplay between PD-1 inhibition and T cell metabolism is not well studied. We found that both murine and human alloreactive T cells concomitantly upregulated PD-1 expression and increased levels of reactive oxygen species (ROS) following allogeneic bone marrow transplantation. This PD-1(Hi)ROS(Hi) phenotype was specific to alloreactive T cells and was not observed in syngeneic T cells during homeostatic proliferation. Blockade of PD-1 signaling decreased both mitochondrial H2O2 and total cellular ROS levels, and PD-1-driven increases in ROS were dependent upon the oxidation of fatty acids, because treatment with etomoxir nullified changes in ROS levels following PD-1 blockade. Downstream of PD-1, elevated ROS levels impaired T cell survival in a process reversed by antioxidants. Furthermore, PD-1-driven changes in ROS were fundamental to establishing a cell's susceptibility to subsequent metabolic inhibition, because blockade of PD-1 decreased the efficacy of later F1F0-ATP synthase modulation. These data indicate that PD-1 facilitates apoptosis in alloreactive T cells by increasing ROS in a process dependent upon the oxidation of fat. In addition, blockade of PD-1 undermines the potential for subsequent metabolic inhibition, an important consideration given the increasing use of anti-PD-1 therapies in the clinic.
A Framework for the Integrated Optimization of Charging and Power Management in Plug-in Hybrid Electric Vehicles (2013)

This paper develops a dynamic programming (DP)-based framework for simultaneously optimizing the charging and power management of a plug-in hybrid electric vehicle (PHEV). These two optimal control problems relate to activities of the PHEV on the electric grid (i.e., charging) and on the road (i.e., power management). The proposed framework solves these two problems simultaneously to avoid loss of optimality resulting from solving them separately. The framework furnishes optimal trajectories of PHEV states and control inputs over a 24-h period. We demonstrate the framework for 24-h scenarios with two driving trips and different power grid generation mixes. The results show that addressing the aforementioned optimization problems simultaneously can elucidate valuable insights. For example, for the chosen daily driving scenario, grid generation mixes, and optimization objective, it is shown that it is not always optimal to completely charge a battery before each driving trip. In addition, reduction in CO 2 resulting from the synergistic interaction of PHEVs with an electric grid containing a significant amount of wind power is studied. The main contribution of this paper to the literature is a framework that makes it possible to evaluate tradeoffs between charging and on-road power management decisions.
Sub-SAT: a formulation for relaxed boolean satisfiability with applications in routing (2003)

Advances in methods for solving Boolean satisfiability (SAT) for large problems have motivated recent attempts to recast physical design problems as Boolean SAT problems. One persistent criticism of these approaches is their inability to supply partial solutions, i.e., to satisfy most but not all of the constraints cast in the SAT style. In this paper, we present a formulation for "subset satisfiable" Boolean SAT: we transform a "strict" SAT problem with N constraints into a new, "relaxed" SAT problem which is satisfiable just if not more than k/spl Lt/N of these constraints cannot be satisfied in the original problem. We describe a transformation based on explicit thresholding and counting for the necessary SAT relaxation. Examples from field-programmable gate-array routing show how we can determine efficiently when we can satisfy "almost all" of our geometric constraints.
Genome-wide risk prediction of common diseases across ancestries in one million people (2022)

Polygenic risk scores (PRS) measure genetic disease susceptibility by combining risk effects across the genome. For coronary artery disease (CAD), type 2 diabetes (T2D), and breast and prostate cancer, we performed cross-ancestry evaluation of genome-wide PRSs in six biobanks in Europe, the United States, and Asia. We studied transferability of these highly polygenic, genome-wide PRSs across global ancestries, within European populations with different health-care systems, and local population substructures in a population isolate. All four PRSs had similar accuracy across European and Asian populations, with poorer transferability in the smaller group of individuals of African ancestry. The PRSs had highly similar effect sizes in different populations of European ancestry, and in early- and late-settlement regions with different recent population bottlenecks in Finland. Comparing genome-wide PRSs to PRSs containing a smaller number of variants, the highly polygenic, genome-wide PRSs generally displayed higher effect sizes and better transferability across global ancestries. Our findings indicate that in the populations investigated, the current genome-wide polygenic scores for common diseases have potential for clinical utility within different health-care settings for individuals of European ancestry, but that the utility in individuals of African ancestry is currently much lower.
Controlled synthesis of bright and compatible lanthanide-doped upconverting nanocrystals (2023)

Certain nanocrystals possess exceptional optical properties that may make them valuable probes for biological imaging, but rendering these nanoparticles biocompatible requires that they be small enough not to perturb cellular systems. This invention describes a phosphorescent upconverting sub-10 nm nanoparticle comprising a lanthanide-doped hexagonal .beta.-phase NaYF.sub.4 nanocrystal and methods for making the same.
Novel Calcium-Binding Ablating Mutations Induce Constitutive RET Activity and Drive Tumorigenesis (2022)

Comprehensive proteogenomic and in silico analyses of a vast number of VUSs identify a novel set of oncogenic and druggable mutations in the well-characterized RET oncogene.
Magnetoencephalography-directed surgery in patients with neocortical epilepsy (2002)

Magnetic source imaging can provide unique localization information that is not available when other noninvasive methods are used. Magnetic source imaging appears most useful for cases of neocortical epilepsy. In particular, when an MS imaging study revealed six or more interictal spikes that were densely clustered in a single anatomical location, the MS image was highly correlated with the zone of seizure origin identified by ECoG. In these cases the MS imaging data may be useful to guide placement of intracranial electrodes.
Interleukin-37 Expression Is Increased in Chronic HIV-1-Infected Individuals and Is Associated with Inflammation and the Size of the Total Viral Reservoir (2015)

Interleukin-37 (IL-37) is a recently identified cytokine with potent antiinflammatory and immunosuppressive functions. The objective of this study was to compare levels of IL-37 mRNA in immunological subgroups of chronic human immunodeficiency virus-1 (HIV-1)-infected individuals and noninfected controls, to determine IL-37's association with biomarkers of inflammation and reservoir size. This was a cross-sectional study. The HIV-1-infected patients were categorized in three subgroups depending on their combination antiretroviral therapy (cART) treatment status and CD4(+) T-cell count. Quantitative RT-PCR was used for the detection of IL-37 mRNA and HIV-1 DNA in peripheral blood mononuclear cells (PBMCs). Biomarkers in plasma were quantified by enzyme-linked immunosorbent assay (ELISA), whereas T-cell activation was determined by flow cytometry. Lastly, lipopolysaccharide (LPS) stimulations of patients PBMCs were carried out to determine differences in IL-37 mRNA response between the subgroups. Sixty HIV-1-infected patients and 20 noninfected controls were included in the study. Steady-state IL-37 mRNA levels in PBMCs were significantly higher in HIV-1-infected individuals compared with noninfected controls: 2.4-fold (p ≤ 0.01) cART-naïve subjects; 3.9-fold (p ≤ 0.0001) inadequate immunological responders; and 4.0-fold (p ≤ 0.0001) in immunological responders compared with non-infected controls. Additionally, levels of the monocyte inflammatory marker sCD14 correlated with IL-37 mRNA (p = 0.03), whereas there was no association with T-cell activation. Finally, we observed a significant correlation between total viral HIV-1 DNA and IL-37 mRNA in PBMCs (p < 0.0001). Collectively, our data shows that the level of IL-37 mRNA is affected by chronic HIV-1-infection. A relationship with the activation of the monocyte compartment is suggested by the correlation with sCD14 and, interestingly, IL-37 could be related to the size of the total viral HIV-1 reservoir.
Hypothyroidism and Levothyroxine-responsive Liver Dysfunction in a Patient with Ring Chromosome 18 Syndrome (2012)

Background: Ring chromosome 18 [r(18)] is a rare constitutional chromosomal aberration syndrome, characterized by dysmorphic face, hypoactivity, short stature, and delayed development.Autoimmune thyroiditis and immunoglobulin (Ig) A deficiency are occasionally associated with chromosome-18 deletion syndromes.Summary: Here, we report a 2-year-old male child with r(18) syndrome and a selective IgA deficiency ( < 1.6 mg/ dL, reference range [rr]: 20-149), who developed hypothyroidism and liver dysfunction.Thyroid function tests (thyroid-stimulating hormone [TSH]: 1031 lIU/mL, rr 0.43-4.0;free triiodothyronine: 0.52 pg/mL, rr 2.37-4.65;free thyroxine: 0.11 ng/dL, rr 1.03-2.00)and positive thyroid antibodies (anti-TSH receptor 1.7 IU/L, cut-off index [coi]: < 1.0, antithyroid peroxidase 171 IU/mL, coi < 0.3, and antithyroglobulin 2.8 IU/mL, coi < 0.3) indicated autoimmune hypothyroidism.Elevated levels of aspartate aminotransferase (AST, 240 IU/L, rr 17-39) and alanine aminotransferase (ALT, 315 IU/L, rr 4-23), but negative antibodies against LKM and mitochondrial M2, suggested no autoimmune hepatitis.Transaminase levels became normalized after he was given levothyroxine therapy to achieve the euthyroid state, but they repeatedly became elevated when levothyroxine was inadvertently discontinued (peak AST = 409 IU/L; peak ALT = 390 IU/L).A maintenance dose of levothyroxine has effectively maintained the euthyroid state and normalized liver function tests despite no immunosuppressive therapy.Conclusions: The r(18) patient with autoimmune hypothyroidism and IgA deficiency suffered from idiopathic hepatitis.The liver dysfunction was associated with hypothyroidism that resolved with thyroid hormone treatment.While the former combination has been described, the latter has not.The reason for the development of hepatitis in association with hypothyroidism is unexplained.However, we postulate that it might be related, in ways that are not clear, to the deleted genes of r(18).
Extended ellipse-line-ellipse trajectory for long-object cone-beam imaging with a mounted C-arm system (2016)

Recent reports show that three-dimensional cone-beam (CB) imaging with a floor-mounted (or ceiling-mounted) C-arm system has become a valuable tool in interventional radiology. Currently, a circular short scan is used for data acquisition, which inevitably yields CB artifacts and a short coverage in the direction of the patient table. To overcome these two limitations, a more sophisticated data acquisition geometry is needed. This geometry should be complete in terms of Tuy's condition and should allow continuous scanning, while being compatible with the mechanical constraints of mounted C-arm systems. Additionally, the geometry should allow accurate image reconstruction from truncated data. One way to ensure such a feature is to adopt a trajectory that provides full R-line coverage within the field-of-view (FOV). An R-line is any segment of line that connects two points on a source trajectory, and the R-line coverage is the set of points that belong to an R-line. In this work, we propose a novel geometry called the extended ellipse-line-ellipse (ELE) for long-object imaging with a mounted C-arm system. This trajectory is built from modules consisting of two elliptical arcs connected by a line. We demonstrate that the extended ELE can be configured in many ways so that full R-line coverage is guaranteed. Both tight and relaxed parametric settings are presented. All results are supported by extensive mathematical proofs provided in appendices. Our findings make the extended ELE trajectory attractive for axially-extended FOV imaging in interventional radiology.
Pareto Optimal Binaural MVDR Beamformer with Controllable Interference Suppression (2022)

The objective of binaural multi-microphone speech enhancement algorithms can be viewed as a multi-criteria design problem as there are several requirements to be met. When applying distortionless beamforming, it is necessary to suppress interfering sources and ambient background noise, and to extract an undistorted replica of the target source. In the binaural versions, it is also important to preserve the binaural cues of the target and the interference sources. In this paper, we propose a unified Pareto optimization framework for binaural distortionless beamformers, which is achieved by defining a multi-objective problem (MOP) to control the amount of interference suppression and noise reduction simultaneously. The derivation is given for the multi-interference case by introducing separate mean squared error (MSE) cost functions for each of the respective interference sources and the background noise. A Pareto optimal set of solutions is provided for any set of parameters. The performance of the proposed method in a noisy and reverberant environment is presented, demonstrating the impact of the trade-off parameters using real-signal recordings.
Synthesis and Reactivity of Aryl Nitrogen Mustard−Oligodeoxyribonucleotide Conjugates (1998)

A versatile method is described for preparing aryl nitrogen mustard-oligodeoxyribonucleotide (mustard-ODN) conjugates under anhydrous conditions. The chemistry uses DMSO soluble triethylammonium or tributylammonium salts of the ODNs. A G/A motif triplex forming ODN was chosen for study since it had been shown earlier to bind with high affinity and specificity to a duplex DNA target. A 5'-hexylamine derivative of this ODN was reacted with three different 2,3,5,6-tetrafluorophenyl ester derivatives of aryl nitrogen mustards which were designed to have different alkylation rates. An HPLC assay was used to determine reaction rates of these mustard-ODNs under various conditions. The reactivity of the mustard groups depended on chloride concentration and the presence of nucleophiles. Conjugation of mustards to G/A-containing ODNs decreased their aqueous stability. Hydrolysis and alkylation rates of these agents were consistent with reaction via an aziridinium intermediate. Rates of sequence specific alkylation within a triplex were determined by denaturing gel electrophoresis and shown to depend on inherent reactivity of the mustard group. The improved synthesis and chemical characterization of mustard-ODNs should facilitate their use as sequence specific alkylating agents and as probes for nucleic acid structure.
Halogen-Transport Atomic-Layer Epitaxy of Cubic GaN Monitored by In Situ Gravimetric Method (1999)

In situ gravimetric monitoring (GM) of atomic-layer epitaxy (ALE) of cubic GaN on a GaN buffer layer/GaAs (001) is investigated using a halogen-transport system with GaCl and NH 3 sources. The cubic GaN growth rate of one monolayer/cycle is obtained at a temperature ranging from 350 to 400°C. It is found that pure cubic GaN can be grown by halogen transport ALE. The growth rate decreases with increasing growth temperature, and a constant growth rate of about 0.45 is observed from 410 to 550°C. In this paper, it is shown that the in situ GM method is a powerful tool for understanding growth mechanism of the group III nitrides, as well as that of GaAs.
[Haploidentical stem cell transplantation for acute myeloid leukemia associated with adult-onset Shwachman-Diamond syndrome]. (2022)

A 21-year-old man presented with bone marrow failure, short stature, fatty degeneration of the pancreas on CT images, and Shwachman-Bodian-Diamond syndrome (SBDS) gene abnormalities (exon 2: c.258+2T>C and deletion of exon 3). Thus, the patient was diagnosed with Shwachman-Diamond syndrome (SDS). In the clinical course, the patient developed acute myeloid leukemia (AML). Hematopoietic stem cell transplantation from the human-leukocytic-antigen-haploidentical father of the patient was performed. The patient was conditioned with 150 mg/m<sup>2</sup> fludarabine, 6.4 mg/kg busulfan, and 4 Gy total body irradiation. Graft-versus-host disease prophylaxis included tacrolimus, micophenolate mofetil, and posttransplant cyclophosphamide. Although the patient achieved a complete remission on day 21, AML relapsed on day 434 after the transplantation. He died of sepsis. The prognosis of patients with SDS and AML is poor. Adult-onset cases must be recognized, and transplantation should be performed during bone marrow failure.
High Dynamic Range Display Systems (2023)

The dynamic range of many real-world environments exceeds the capabilities of current display technology by several orders of magnitude. In this paper we discuss the design of two different display systems that are capable of displaying images with a dynamic range much more similar to that encountered in the real world. The first display system is based on a combination of an LCD panel and a DLP projector, and can be built from off-the-shelf components. While this design is feasible in a lab setting, the second display system, which relies on a custom-built LED panel instead of the projector, is more suitable for usual office workspaces and commercial applications. We describe the design of both systems as well as the software issues that arise. We also discuss the advantages and disadvantages of the two designs and potential applications for both systems.
Protein‐Kinase C Mediates MCH Signal Transduction in Teleost, Synbranchus marmoratus, Melanocytes (1991)

MCH (melanin concentrating hormone) is a heptadecapeptide, Asp-Thr-Met-Arg-Cys-Met-Val-Gly-Arg-Val-Tyr-Arg-Pro-Cys-Trp-Glu-Val, which stimulates melanosome (melanin granule) aggregation to a perinuclear position within teleost fish integumental melanocytes, resulting in lightening of the skin. The mechanisms of action of MCH are unknown. Drugs that affect the diacylglycerol/inositol triphosphate pathway were used to investigate the possible roles of this pathway in the mechanisms of action of MCH on Synbranchus marmoratus (teleost) melanocytes. The shift of the dose-response curve to MCH in the presence of various concentrations of 4-bromophenacyl bromide and neomycin sulphate, phospholipase C inhibitors, suggests that phospholipase C is stimulated after MCH receptor activation. Low concentrations (10(-9) to 10(-8) M) of the phorbol ester TPA exhibited MCH-like activity, eliciting a dose-dependent melanosome aggregation. Higher doses, however, displaced to the right the dose-response curve to MCH, as did the protein kinase C inhibitors, dibucaine and 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine (H-7). These results support the assumption that protein kinase C mediates the pigment aggregating activity of MCH. Both MCH and norepinephrine lightening actions were abolished by beta-glycerophosphate, a phosphatase inhibitor, suggesting that a protein dephosphorylation occurs during melanosome aggregation, and is, therefore, a common event triggered by MCH and norepinephrine, although both agonists act through separate receptors and exhibit different transduction mechanisms.
Receptor-specific allelic exclusion of TCRV alpha-chains during development. (1998)

Expression of a single Ag receptor on lymphocytes is maintained via allelic exclusion that generates cells with a clonal receptor repertoire. We show in normal mice and mice expressing functionally rearranged TCR alphabeta transgenes that allelic exclusion at the TCR alpha locus is not operational in immature thymocytes, whereas most mature T cells express a single TCRV alpha-chain. TCRV alpha allelic exclusion in mature thymocytes is regulated through a CD45 tyrosine phosphatase-mediated signal during positive selection. Using functional and genetic systems for selection of immature double TCRV alpha+ thymocytes, we show that peptide-specific ligand recognition provides the signal for allelic exclusion, i.e., mature T cells maintain expression of the ligand-specific TCRV alpha-chain, but lose the nonfunctional receptor. Whereas activation of TCRV beta-chains or CD3epsilon leads to receptor internalization, TCRV alpha ligation promotes retention of the TCR on the cell surface. Although both TCRV alpha- and TCRV beta-chains trigger phosphotyrosine signaling, only the TCRV beta-chain mediates membrane recruitment of the GTPase dynamin. These data indicate that TCRV alpha-directed signals for positive selection control allelic exclusion in T cells, and that developmental signals can select for single receptor usage.