gebhart/patrepeval huggingface dataset:
Involvement of Distinct Cellular Compartments in the Abnormal Lymphoid Organogenesis in Lymphotoxin-α-Deficient Mice and Alymphoplasia ( aly ) Mice Defined by the Chimeric Analysis (1999)

Abstract Both lymphotoxin-α (LTα)-deficient mice and alymphoplasia (aly) mice, a natural mutant strain, manifest a quite similar phenotype: lack of lymph nodes (LN) and Peyer’s patches (PP), with disturbed spleen architecture. The mechanisms underlying the defective lymphoid organogenesis in these mice were investigated by generating aggregation chimeras; ex vivo fused morulae were implanted into pseudo-pregnant host females and allowed to develop to term. Chimeric mice between LTα-deficient mice and wild-type mice restored LN and PP almost completely, suggesting that LTα expressed by circulating bone marrow-derived cells is essential for lymphoid organogenesis as well as for organization of spleen architecture. By contrast, chimeric mice between aly mice and wild-type mice showed only limited restoration of LN and PP. This suggests that the putative aly gene product does not act as a circulating ligand for lymphoid organogenesis, like LTα. Rather, abnormal development of lymphoid organs in aly mice seems most likely due to the defective development of the incipient stromal cells of the LN and PP. Supporting this hypothesis, up-regulation of VCAM-1 on aly mouse embryonic fibroblasts by signals through LTβR, which is exclusively expressed by nonlymphoid cells, was disturbed. These studies demonstrate that LTα and the putative aly gene product together control lymphoid organogenesis with a close mechanistic relationship in their biochemical pathways through governing the distinct cellular compartments, the former acting as a circulating ligand and the latter as a LTβR-signaling molecule expressed by the stroma of the lymphoid organs.
A boundary element approach for image‐guided near‐infrared absorption and scatter estimation (2007)

Multimodality NIR spectroscopy systems offer the possibility of region-based vascular and molecular characterization of tissue in vivo. However, computationally efficient 3D image reconstruction algorithms specific to these image-guided systems currently do not exist. Image reconstruction is often based on finite-element methods (FEMs), which require volume discretization. Here, a boundary element method (BEM) is presented using only surface discretization to recover the optical properties in an image-guided setting. The reconstruction of optical properties using BEM was evaluated in a domain containing a 30 mm inclusion embedded in two layer media with different noise levels and initial estimates. For 5% noise in measurements, and background starting values for reconstruction, the optical properties were recovered to within a mean error of 6.8%. When compared with FEM for this case, BEM showed a 28% improvement in computational time. BEM was also applied to experimental data collected from a gelatin phantom with a 25 mm inclusion and could recover the true absorption to within 6% of expected values using less time for computation compared with FEM. When applied to a patient-specific breast mesh generated using MRI, with a 2 cm ductal carcinoma, BEM showed successful recovery of optical properties with less than 5% error in absorption and 1% error in scattering, using measurements with 1% noise. With simpler and faster meshing schemes required for surface grids as compared with volume grids, BEM offers a powerful and potentially more feasible alternative for high-resolution 3D image-guided NIR spectroscopy.
Laboratory, Clinical, and Kindergarten Test of a New Eccentric Infrared Photorefractor (PowerRefractor) (2000)

The PowerRefractor was shown to have comparable or slightly better reliability and accuracy than a modern autorefractor; however, it has major advantages over current autorefractors in that it is faster, measures both eyes at once, and gives interpupillary distance, pupil size, and information on the alignment of the eyes at the same time.
ChemInform Abstract: Synthesis of Either Enantiomer of cis‐3‐Aminocyclopentanecarboxylic Acid from Both Enantiomers of Racemic 2‐Azabicyclo(2.2.1)hept‐5‐en‐3‐ one. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure Legends from Mechanism, Consequences, and Therapeutic Targeting of Abnormal IL15 Signaling in Cutaneous T-cell Lymphoma (2023)

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High-dose methotrexate with leucovorin rescue in patients with unresectable non-small cell carcinoma of the lung (1983)

Thirty-one patients with unresectable non-small cell carcinoma of the lung (19 adenocarcinoma, 7 large cell carcinoma, 4 squamous cell carcinoma, 1 mixed histology) were treated with one of two intravenous infusion schedules of high dose methotrexate with leucovorin rescue. First, 14 patients received methotrexate in escalating doses from 1.5 to 12 g/m2 over 6 hours followed immediately with leucovorin 15 mg/m2 for 12 doses every 6 hours; there were no complete or partial responses among these 14 patients. Then, 17 patients were treated with a loading bolus of 50 mg/m2 intravenous methotrexate followed by a 30-hour continuous infusion of 1.5 g/m2. Leucovorin 15 mg/m2 every 6 hours for 12 doses was begun at the end of the infusion. There were 3 partial responses among the 17 patients in this group. The results demonstrate that both 6- and 30-hour infusions of high-dose methotrexate regimens can be given safely to middle aged adult patients, but the overall 10% response rate does not appear to be significantly different than the results with standard-dose methotrexate.
Directed evolution of a picomolar-affinity, high-specificity antibody targeting phosphorylated tau (2018)

Antibodies are essential biochemical reagents for detecting protein post-translational modifications (PTMs) in complex samples. However, recent efforts in developing PTM-targeting antibodies have reported frequent nonspecific binding and limited affinity of such antibodies. To address these challenges, we investigated whether directed evolution could be applied to improve the affinity of a high-specificity antibody targeting phosphothreonine 231 (pThr-231) of the human microtubule-associated protein tau. On the basis of existing structural information, we hypothesized that improving antibody affinity may come at the cost of loss in specificity. To test this hypothesis, we developed a novel approach using yeast surface display to quantify the specificity of PTM-targeting antibodies. When we affinity-matured the single-chain variable antibody fragment through directed evolution, we found that its affinity can be improved >20-fold over that of the WT antibody, reaching a picomolar range. We also discovered that most of the high-affinity variants exhibit cross-reactivity toward the nonphosphorylated target site but not to the phosphorylation site with a scrambled sequence. However, systematic quantification of the specificity revealed that such a tradeoff between the affinity and specificity did not apply to all variants and led to the identification of a picomolar-affinity variant that has a matching high specificity of the original phosphotau antibody. In cell- and tissue-imaging experiments, the high-affinity variant gave significantly improved signal intensity while having no detectable nonspecific binding. These results demonstrate that directed evolution is a viable approach for obtaining high-affinity PTM-specific antibodies and highlight the importance of assessing the specificity in the antibody engineering process.
Evidence for in vitro extensive proliferation of adult hepatocytes and biliary epithelial cells (2023)

Over the last several years, a method has emerged which endows adult hepatocytes with <i>in vitro</i> proliferative capacity, producing chemically-induced liver progenitors (CLiPs). However, a recent study questioned the origin of these cells, suggesting that resident liver progenitor cells, but not hepatocytes, proliferate. Here, we provide lineage tracing-based evidence that adult hepatocytes acquire proliferative capacity <i>in vitro</i> . Unexpectedly, we also found that the CLiP method allows biliary epithelial cells to acquire extensive proliferative capacity. Interestingly, after long-term culture, hepatocyte-derived cells (hepCLiPs) and biliary-derived cells (bilCLiPs) become similar in their gene expression patterns, and they both exhibit differentiation capacity to form hepatocyte-like cells. Finally, we provide evidence that hepCLiPs can repopulate chronically injured mouse livers, reinforcing our earlier argument that CLiPs can be a cell source for liver regenerative medicine. Moreover, this study offers bilCLiPs as a potential cell source for liver regenerative medicine.
Increased carrier mobility in end-functionalized oligosilanes (2015)

We show that a class of oligosilane-arene σ, π-hybrid materials exhibits distinct and enhanced solid-state electronic properties relative to its parent components. In the single crystal structure, the σ-conjugation axis of one molecule points towards the π-face of a neighboring molecule due to an unusual gauche conformation. This organization is hypothesized to be beneficial for charge transport. We show that solution-deposited crystalline films of the hybrid materials show up to a 100-fold increase in space-charge limited current (SCLC) mobility relative to literature reports of photoinduced hole transport in oligosilane films. The discovery that σ, π-hybrids are more than the sum of their parts offers a design opportunity for new materials.
Chromosomal Distribution and Coding Capacity of the Human Endogenous Retrovirus HERV-W Family (2000)

Some genomic elements of the multicopy HERV-W endogenous retroviral family have been previously identified in databases. One of them, located on chromosome 7, contains a single complete open reading frame (ORF) putatively encoding an envelope protein. We have experimentally investigated the genomic complexity and coding capacity of the HERV-W family. The human haploid genome contains at least 70, 100, and 30 HERV-W-related gag, pro, and env regions, respectively, widely and heterogeneously dispersed among chromosomes. Using in vitro transcription-translation procedures, three putative HERV-W gag, pro, and env ORFs were detected on chromosomes 3, 6, and 7, respectively, and their sequences analyzed. A 363 amino acid gag ORF containing matrix and carboxy-terminal truncated capsid domains encoded a putative 45-kDa protein. No gag-pro ORF was found, but a pro sequence containing a DTG active site was detected. Finally, the previously described 538 amino acid HERV-W env ORF, located on chromosome 7, was shown to be unique and encoded a putative 80-kDa glycosylated protein. Proteins of molecular mass identical to the one obtained by an in vitro transcription-translation procedure were detected in human placenta, using anti HERV-W Gag- and Env-specific antibodies. The absence of an HERV-W replication-competent provirus versus the existence of HERV-W-related Gag and Env proteins in healthy human placenta is discussed with respect to particle formation, physiology, and pathology.
Core losses under DC bias condition based on Steinmetz parameters (2010)

When designing inductive components, calculating core losses is a difficult and not yet entirely solved problem. In particular it is impossible to predict the influence of a DC premagnetization on the losses without performing extensive measurements. For this work, different materials have been tested to gain information how core losses are influenced by a premagnetization. Measurements on molypermalloy powder, silicon steel, nanocrystalline material, and ferrite cores have been performed. Of the tested materials, a premagnetization mainly influences losses in ferrites and nanocrystalline materials, whereas the influence of a premagnetization in molypermalloy powder cores, and cores of silicon steel is negligible. The Steinmetz Premag-netization Graph (SPG) that shows the dependency of the Steinmetz parameters (α, β and k) on premagnetization is introduced. This permits the calculation of core losses under DC bias conditions. Such graphs are given for different materials and different operating temperatures. In addition, a detailed description of the test system is given, as high accuracy is crucial.
Layout study of contactless magnetoresistor current sensor for high frequency converters (2016)

In this paper, we present a new technique to unify and intensify the magnetic fields that results in higher performance of Anisotropic Magneto-Resistive (AMR) current sensors and consequently develop a closed loop controller for 100W synchronous GaN buck converter at 1MHz. The closed loop operation of high switching frequency converters at high power has always been a big challenge due to lack of access to current information. The proposed method that also intensifies the magnetic fields through the sensor, significantly improves the bandwidth limits, and reduces electromagnetic interference (EMI) on AMR sensors, making them applicable for high switching frequency and high current power electronics converters. After verifying uniform distribution concept through simulation, we also implemented a prototype of AMR current sensors onto Printed Circuit Board (PCB) for verification of the concept at high frequency converter. We then present the design procedure and associated challenges of an integrated analogue peak current controller for creating the closed loop operation of a GaN buck converter at high switching frequency.
Molecular orientation within thin films of isomorphic molecular semiconductors (2015)

Subtle structural variation of isomorphic molecular semiconductors leads to sharp contrast in electronic structures and molecular orientation in the bulk.
Second Spine: A device to relieve stresses on the upper body during loaded walking (2014)

The target of this work is to experimentally validate the Second Spine, a wearable device recently developed by our group to transfer forces from shoulder to pelvis during loaded walking. A key-feature of the Second Spine compared to traditional framed backpacks is the adjustable stiffness of its structure, which allows the wearer to change the load-bearing behavior of the device. In line with previous studies on loaded walking, we investigate biomechanical and physiological variables on a small group of young healthy subjects, as they walked on a treadmill under 3 different conditions: free walking, walking with a backpack of 25% of subject's Body Weight (BW), and walking with the same backpack while wearing the device. Results indicate that wearing the Second Spine significantly reduces the pressure on shoulders and induces smaller deviations from unloaded walking in terms of gait timing and stride length. The activations of the rectus femoris and the gastrocnemius muscles, along with the kinematics of the knee joint, provide indirect evidence that dynamic loads were rigidly transmitted from the shoulder to the waist. We discuss how these preliminary findings might be relevant for the prevention of injuries related to load carriage, and how they set important guidelines for the next generation of the Second Spine.
Response Rates of Patients With Metastatic Melanoma to High-Dose Intravenous Interleukin-2 After Prior Exposure to Alpha-Interferon or Low-Dose Interleukin-2 (2002)

We evaluated 567 patients with metastatic melanoma who were treated with high-dose intravenous interleukin-2 (IL-2) to determine whether prior treatment with either alpha-interferon or low-dose IL-2 altered the rates of response to subsequent high-dose IL-2. Of the 567 patients treated, 46 patients had received low-dose IL-2 before, and 78 had received alpha-interferon before. The response rate for patients who had received IL-2 before compared with IL-2 naïve patients was 15% versus 21% respectively (p = 0.39). The response rate for patients who had received alpha-interferon before compared with patients who had not was 13% versus 21% (p = 0.084). Therefore, prior low-dose IL-2 therapy does not appear to prevent a subsequent response to high-dose IL-2. There is a trend for patients who received alpha-interferon before to have a lower-response rate to subsequent high-dose IL-2, but the number of patients evaluated in this study is too small to definitively answer this question.
Quantitative Physical Fitness Measures Inversely Associated With Myopia Severity in Military Males: The CHIEF Study (2019)

Myopia has been linked to body weight and sedentary status, but the association with quantitatively measured physical fitness in adults has not been examined. Cross-sectional analyses were performed to investigate the association between physical fitness and myopia in 3,669 military men (aged 29.4 years) in Taiwan. The severity of myopia obtained from the left eye was classified as mild (-0.5 to -3.0 diopters; <i>n</i> = 544), moderate -3.1 to -6.0 diopters; <i>n</i> = 563), and high (<-6.0 diopters; <i>n</i> =150); others were defined as nonmyopia (<i>n</i> = 2,412). Aerobic fitness was evaluated by time for a 3000-meter run test, and muscular endurance was evaluated by numbers of 2-min sit-ups and 2-min push-ups. A value of <i>p</i> < .0125 was considered significant. A multiple linear regression analysis was used to determine the relationship. Individuals who were less physically fit had higher risk of myopia. The associations were dose-dependently significant with mild, moderate, and high myopia for 3000-meter running time (β = 9.64; 95% confidence intervals [3.22, 16.05], β = 12.41; 95% CI [6.05, 18.76], and β = 20.87; 95% CI [9.22, 32.51], respectively) after controlling for the potential covariates. There tended to be an inverse association with moderate and high myopia for numbers of 2-min push-ups (β = -1.38; 95% CI [-2.43, -0.34] and β = -2.10; 95% CI [- 3.97, -0.22], respectively) and 2-min sit-ups (β = -0.83; 95% CI [-1.54, -0.12] and β = -1.29; 95% CI [-2.56, -0.02], respectively), respectively. This study suggested that physical fitness, particularly aerobic fitness of the military males who received regular training, is inversely associated with myopia severity, independent of service specialty, body mass index, and educational level.
CHAT to Your Destination (2007)

Fuliang Weng, Baoshi Yan, Zhe Feng, Florin Ratiu, Madhuri Raya, Brian Lathrop, Annie Lien, Sebastian Varges, Rohit Mishra, Feng Lin, Matthew Purver, Harry Bratt, Yao Meng, Stanley Peters, Tobias Scheideck, Badri Raghunathan, Zhaoxia Zhang. Proceedings of the 8th SIGdial Workshop on Discourse and Dialogue. 2007.
Reference Managers that Support Collaborative Research: Dreaming of the Perfect Fit (2018)

Reference or citation managers aid in capturing and managing citations and associated full text, tracking references and citing them properly in manuscripts, and creating bibliographies. With more features than ever, selecting the most appropriate reference manager can be overwhelming for users and librarians. One common situation in which librarians are asked for advice involves building shared libraries of references to support collaborative group work. This project developed a structured evaluation for comparison of several common citation managers and prototypical use cases to help match features with user needs, preferences, and workflows. As products evolve and needs change, is there a "perfect fit"?
Enantioselective Cyclizations of Silyloxyenynes Catalyzed by Cationic Metal Phosphine Complexes (2012)

The discovery of complementary methods for enantioselective transition metal-catalyzed cyclization with silyloxyenynes has been accomplished using chiral phosphine ligands. Under palladium catalysis, 1,6-silyloxyenynes bearing a terminal alkyne led to the desired five-membered ring with high enantioselectivities (up to 91% ee). As for reactions under cationic gold catalysis, 1,6- and 1,5-silyloxyenynes bearing an internal alkyne furnished the chiral cyclopentane derivatives with excellent enantiomeric excess (up to 94% ee). Modification of the substrate by incorporating an α,β-unsaturation led to the discovery of a tandem cyclization. Remarkably, using silyloxy-1,3-dien-7-ynes under gold catalysis conditions provided the bicyclic derivatives with excellent diastereo- and enantioselectivities (up to >20:1 dr and 99% ee).
Evolutionary Expansion of the Amidohydrolase Superfamily in Bacteria in Response to the Synthetic Compounds Molinate and Diuron (2015)

The amidohydrolase superfamily has remarkable functional diversity, with considerable structural and functional annotation of known sequences. In microbes, the recent evolution of several members of this family to catalyze the breakdown of environmental xenobiotics is not well understood. An evolutionary transition from binuclear to mononuclear metal ion coordination at the active sites of these enzymes could produce large functional changes such as those observed in nature, but there are few clear examples available to support this hypothesis. To investigate the role of binuclear-mononuclear active-site transitions in the evolution of new function in this superfamily, we have characterized two recently evolved enzymes that catalyze the hydrolysis of the synthetic herbicides molinate (MolA) and phenylurea (PuhB). In this work, the crystal structures, mutagenesis, metal ion analysis, and enzyme kinetics of both MolA and PuhB establish that these enzymes utilize a mononuclear active site. However, bioinformatics and structural comparisons reveal that the closest putative ancestor of these enzymes had a binuclear active site, indicating that a binuclear-mononuclear transition has occurred. These proteins may represent examples of evolution modifying the characteristics of existing catalysts to satisfy new requirements, specifically, metal ion rearrangement leading to large leaps in activity that would not otherwise be possible.
Semipolar {202¯1} GaN Edge-Emitting Laser Diode on Epitaxial Lateral Overgrown Wing (2021)

Edge-emitting laser diodes (LDs) were fabricated on a reduced dislocation density epitaxial lateral overgrown (ELO) wing of a semipolar {202¯1} GaN substrate, termed an ELO wing LD. Two types of facet feasibility studies were conducted: (1) “handmade” facets, wherein lifted-off ELO wing LDs were cleaved manually, and (2) facets formed on wafers through reactive ion etching (RIE). Pulsed operation electrical and optical measurements confirmed the laser action in the RIE facet LDs with a threshold current of ~19 kAcm−2 and maximum light output power of 20 mW from a single uncoated facet. Handmade facet devices showed spontaneous, LED-like emission, confirming device layers remain intact after mechanical liftoff.