gebhart/patrepeval huggingface dataset:
Detection of Cell-CAM 105 in the pericanalicular domain of the rat hepatocyte plasma membrane (1991)

Cell-CAM 105 has been identified as a cell adhesion molecule based on the ability of anti-cell-CAM 105 monospecific Fab fragments to inhibit the reaggregation of rat hepatocytes. Because of its adhesive properties, it was expected that cell-CAM 105 would be present on the lateral cell surface where adhesive interactions predominate. Paradoxically, however, immunofluorescence analysis of frozen sections of rat liver using specific monoclonal antibodies indicated that cell-CAM 105 was present exclusively in the bile canalicular domain of the rat hepatocyte where there is no intercellular adhesion. To more precisely define the in situ localization of cell-CAM 105, immunoperoxidase labeling and electron microscopy were used to examine intact and mechanically dissociated liver tissue. Results showed that when accessibility was provided by mechanical dissociation of perfusion fixed liver tissue, cell-CAM 105 could be detected in the pericanalicular region of lateral membranes. In contrast, when hepatocytes were labeled after incubation in vitro under conditions used during adhesion assays to induce reaggregation, cell-CAM 105 rapidly redistributed to all areas of the plasma membrane. Immunofluorescence analysis of primary hepatocyte cultures further revealed that cell-CAM 105 and two other bile canalicular proteins relocalized to discrete domains reminiscent of bile canaliculi, whereas cell-CAM 105 was also present in areas of intercellular contact. Serial section electron microscopy analysis of well-defined, cross-sectional profiles of bile canaliculi suggested the presence of cell-CAM 105-positive membrane folds that extended along the length of the bile canalicular border. In sections from livers in which calcium-dependent adhesive contacts had been disrupted by treatment with ethylenediamine tetraacetate, intact bile canaliculi were found that remained attached only by these border folds. The implications of these results are discussed with regard to a possible role for cell-CAM 105 in bile canalicular formation.
Handbook of Porphyrin Science (Volumes 31-35): With Applications to Chemistry, Physics, Materials Science, Engineering, Biology and Medicine (2010)

Complete with hundreds of figures, tables and structural formulas, and thousands of literature citations, all researchers and graduate students in this field will find it to be an essential, major reference source now, and for many years to come."--
STM and DFT Investigations of Isolated Porphyrin on a Silicon‐Based Semiconductor at Room Temperature (2009)

Model compound: Individual adsorbed Cu-5,10,15,20-tetrakis(3,5-di-tert-butylphenyl) porphyrins are observed by STM on a Si(111)-B surface with an atomic resolution at room temperature (see figure). The conformational modifications after the adsorption on the surface is successfully interpreted with DFT calculations performed on the entire system (molecule and substrate). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Study of JEDEC Board-Level Drop Test Performance Prediction Trend of BGA Package with SAC1205 Under Different Key Factors (2022)

With the rapid development of technology, the number and demand for handheld devices are increasing, and the new technology product development and launch are getting faster and faster. Also, handheld devices need to withstand various movements, fall-down situations, and even regular use in different temperature environments. Therefore, solder joint reliability is decidedly crucial for handheld devices. Moreover, how to seize the critical factors during the design development phase and fulfill market demands are also significant. According to the definition of JESD22-B111 [1], the drop test requires that the board should be horizontal with the package facing in the downward direction (-Z) during the experiment. Therefore, under the influence of the acceleration of gravity, the weight of the ball grid array(BGA) package, the number of balls, solder ball material, and the solder ball pad size in the drop test are recognized as important factors affecting the board-level reliability of the drop test. This study will explore these key factors and how they affect the board-level reliability of the drop test.
Sierra/SolidMechanics 4.46 Goodyear Specific (2017)

This document covers Sierra/SolidMechanics capabilities specific to Goodyear use cases. Some information may be duplicated directly from the Sierra/SolidMechanics User’s Guide but is reproduced here to provide context for Goodyear-specific options.
Cell type-specific activation of metabolism reveals that β-cell secretion suppresses glucagon release from α-cells in rat pancreatic islets (2005)

Abnormal glucagon secretion is often associated with diabetes mellitus. However, the mechanisms by which nutrients modulate glucagon secretion remain poorly understood. Paracrine modulation by beta- or delta-cells is among the postulated mechanisms. Herein we present further evidence of the paracrine mechanism. First, to activate cellular metabolism and thus hormone secretion in response to specific secretagogues, we engineered insulinoma INS-1E cells using an adenovirus-mediated expression system. Expression of the Na+-dependent dicarboxylate transporter (NaDC)-1 resulted in 2.5- to 4.6-fold (P < 0.01) increases in insulin secretion in response to various tricarboxylic acid cycle intermediates. Similarly, expression of glycerol kinase (GlyK) increased insulin secretion 3.8- or 4.2-fold (P < 0.01) in response to glycerol or dihydroxyacetone, respectively. This cell engineering method was then modified, using the Cre-loxP switching system, to activate beta-cells and non-beta-cells separately in rat islets. NaDC-1 expression only in non-beta-cells, among which alpha-cells are predominant, caused an increase (by 1.8-fold, P < 0.05) in glucagon secretion in response to malate or succinate. However, the increase in glucagon release was prevented when NaDC-1 was expressed in whole islets, i.e., both beta-cells and non-beta-cells. Similarly, an increase in glucagon release with glycerol was observed when GlyK was expressed only in non-beta-cells but not when it was expressed in whole islets. Furthermore, dicarboxylates suppressed basal glucagon secretion by 30% (P < 0.05) when NaDC-1 was expressed only in beta-cells. These data demonstrate that glucagon secretion from rat alpha-cells depends on beta-cell activation and provide insights into the coordinated mechanisms underlying hormone secretion from pancreatic islets.
Full efficiency benefits and implementation considerations for cruise altitude and speed optimization in the National Airspace system (2014)

Thesis: S.M., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, 2014.
Antibody Supervised Training of a Deep Learning Based Algorithm for Leukocyte Segmentation in Papillary Thyroid Carcinoma (2020)

The quantity of leukocytes in papillary thyroid carcinoma (PTC) potentially have prognostic and treatment predictive value. Here, we propose a novel method for training a convolutional neural network (CNN) algorithm for segmenting leukocytes in PTCs. Tissue samples from two retrospective PTC cohort were obtained and representative tissue slides from twelve patients were stained with hematoxylin and eosin (HE) and digitized. Then, the HE slides were destained and restained immunohistochemically (IHC) with antibodies to the pan-leukocyte anti CD45 antigen and scanned again. The two stain-pairs of all representative tissue slides were registered, and image tiles of regions of interests were exported. The image tiles were processed and the 3,3'-diaminobenzidine (DAB) stained areas representing anti CD45 expression were turned into binary masks. These binary masks were applied as annotations on the HE image tiles and used in the training of a CNN algorithm. Ten whole slide images (WSIs) were used for training using a five-fold cross-validation and the remaining two slides were used as an independent test set for the trained model. For visual evaluation, the algorithm was run on all twelve WSIs, and in total 238,144 tiles sized 500 × 500 pixels were analyzed. The trained CNN algorithm had an intersection over union of 0.82 for detection of leukocytes in the HE image tiles when comparing the prediction masks to the ground truth anti CD45 mask. We conclude that this method for generating antibody supervised annotations using the destain-restain IHC guided annotations resulted in high accuracy segmentations of leukocytes in HE tissue images.
Anti-tissue transglutaminase antibodies (TG2A) positivity and the risk of vitamin D deficiency among children - a cross-sectional study in the generation R cohort (2023)

Our findings suggest there is no association between TG2A positivity and suboptimal vitamin D status in the general pediatric population. However, the overall prevalence of vitamin D deficiency in both populations was high, suggesting that screening for vitamin D deficiency among children, regardless of TG2A positivity, would be beneficial to ensure early dietary intervention if needed.
PCEP Procedures and Protocol Extensions for Using PCE as a Central Controller (PCECC) for Segment Routing (SR) MPLS Segment Identifier (SID) Allocation and Distribution. (1998)

The Path Computation Element (PCE) is a core component of Software-
Defined Networking (SDN) systems. It can compute optimal paths for
traffic across a network and can also update the paths to reflect
changes in the network or traffic demands. PCE was developed to
derive paths for MPLS Label Switched Paths (LSPs), which are supplied
to the head end of the LSP using the Path Computation Element
Communication Protocol (PCEP). But SDN has a broader applicability
than signaled (G)MPLS traffic-engineered (TE) networks, and the PCE
may be used to determine paths in a range of use cases. PCEP has been
proposed as a control protocol for use in these environments to allow
the PCE to be fully enabled as a central controller. A PCE-based
Central Controller (PCECC) can simplify the processing of a
distributed control plane by blending it with elements of SDN and
without necessarily completely replacing it. Thus, the LSP can be
calculated/set up/initiated and the label forwarding entries can also
be downloaded through a centralized PCE server to each network device
along the path while leveraging the existing PCE technologies as much
as possible. This document specifies the procedures and PCEP
extensions when a PCE-based controller is also responsible for
configuring the forwarding actions on the routers, in addition to
computing the paths for packet flows in a segment routing (SR) network
and telling the edge routers what instructions to attach to packets as
they enter the network. PCECC is further enhanced for SR SID (Segment
Identifier) allocation and distribution.
Reactive oxygen species produced by altered tumor metabolism impacts cancer stem cell maintenance (2021)

Controlling reactive oxygen species (ROS) at sustainable levels can drive multiple facets of tumor biology, including within the cancer stem cell (CSC) population. Tight regulation of ROS is one key component in CSCs that drives disease recurrence, cell signaling, and therapeutic resistance. While ROS are well-appreciated to need oxygen and are a product of oxidative phosphorylation, there are also important roles for ROS under hypoxia. As hypoxia promotes and sustains major stemness pathways, further consideration of ROS impacts on CSCs in the tumor microenvironment is important. Furthermore, glycolytic shifts that occur in cancer and may be promoted by hypoxia are associated with multiple mechanisms to mitigate oxidative stress. This altered metabolism provides survival advantages that sustain malignant features, such as proliferation and self-renewal, while producing the necessary antioxidants that reduce damage from oxidative stress. Finally, disease recurrence is believed to be attributed to therapy resistant CSCs which can be quiescent and have changes in redox status. Effective DNA damage response pathways and/or a slow-cycling state can protect CSCs from the genomic catastrophe induced by irradiation and genotoxic agents. This review will explore the delicate, yet complex, relationship between ROS and its pleiotropic role in modulating the CSC.
Early Life Supraphysiological Levels of Oxygen Exposure Permanently Impairs Hippocampal Mitochondrial Function (2019)

Preterm infants requiring prolonged oxygen therapy often develop cognitive dysfunction in later life. Previously, we reported that 14-week-old young adult mice exposed to hyperoxia as newborns had spatial and learning deficits and hippocampal shrinkage. We hypothesized that the underlying mechanism was the induction of hippocampal mitochondrial dysfunction by neonatal hyperoxia. C57BL/6J mouse pups were exposed to 85% oxygen or room air from P2-P14. Hippocampal proteomic analysis was performed in young adult mice (14 weeks). Mitochondrial bioenergetics were measured in neonatal (P14) and young adult mice. We found that hyperoxia exposure reduced mitochondrial ATP-linked oxygen consumption and increased state 4 respiration linked proton leak in both neonatal and young adult mice while complex I function was decreased at P14 but increased in young adult mice. Proteomic analysis revealed that hyperoxia exposure decreased complex I NDUFB8 and NDUFB11 and complex IV 7B subunits, but increased complex III subunit 9 in young adult mice. In conclusion, neonatal hyperoxia permanently impairs hippocampal mitochondrial function and alters complex I function. These hippocampal mitochondrial changes may account for cognitive deficits seen in children and adolescents born preterm and may potentially be a contributing mechanism in other oxidative stress associated brain disorders.
Pressure tuning of the motional behavior ofLi+,Ag+, andCu+ions in shallow off-center potentials of alkali halides (1979)

The delicate balance of interaction energies, which creates in certain alkali halides a shallow off-center potential for small substitutional defect ions, can be drastically altered by application of relatively small ( 7 kbar) hydrostatic pressure (corresponding to about 1% lattice compression). This has been investigated for KCl: ${\mathrm{Li}}^{+}$, NaBr: ${\mathrm{Cu}}^{+}$, RbCl: ${\mathrm{Ag}}^{+}$, and RbBr: ${\mathrm{Ag}}^{+}$ by measurements of the real and imaginary dielectric response of the off-center dipoles, and by absorption-strength measurements of the ${\mathrm{Ag}}^{+}$ and ${\mathrm{Cu}}^{+}$ forbidden $d\ensuremath{\rightarrow}s$ uv transitions (which become partially allowed in the odd-parity off-center potential). Applied pressure reduces gradually the central and rotational barriers of the multiwell potential and, while keeping the off-center dipole moment constant, drastically increase the dipolar reorientation rates. As a consequence, the observable range of relaxation frequencies (${10}^{2}$-${10}^{5}$ Hz) shifts under pressure to low temperatures, tuning through regimes of thermally activated motion with decreasing barriers into regimes of tunneling motion. Similar to the situation in the superionic conductors, a particular match between cavity and point-ion size produces an optimum "local ionic mobility" at lowest temperatures. Slightly higher lattice compression leads to the disappearance of this ionic mobility, due to a change of the defect potential into a centrosymmetric one. This off- to on-center transition (a "localized analog" to pressure-induced displacive phase transitions in ferroelectrics) is discussed in terms of its first- or second-order character. The question of whether pressure induced changes in the phonon dressing ("polaron effect") of the dipoles can contribute to the observed relaxation changes will be discussed, too.
Selective Deoxygenation of Pyridine N‐Oxides through Photoredox Catalysis of a Dilacunary Silicotungstate (2016)

Abstract In this paper, we report a highly selective and widely applicable method for deoxygenation of pyridine N ‐oxides using ethanol as the reducing agent through the visible‐light‐responsive photoredox catalysis of a divacant lacunary silicotungstate TBA 4 H 4 [γ‐SiW 10 O 36 ] ( I , TBA=tetra‐ n ‐butylammonium). By irradiation with visible light (λ &gt; 385 nm), the two‐electron and two‐proton transfers from the coordinated ethanol to I efficiently took place. Then, the transiently stored electrons and protons within I could be effectively utilized for the selective deoxygenation of pyridine N ‐oxides. Various kinds of structurally diverse pyridine N ‐oxides could be converted into the corresponding substituted pyridines in high yields, even in the presence of other reducible functional groups, such as olefinic, chloro, cyano, carbonyl, and amide groups. In addition, I could be readily retrieved after the reaction, and the retrieved I could be reused with keeping its high catalytic performance. The lacunary site of I played an important dual role as the electron transfer site from ethanol to I and the selective electron transfer site from the reduced I to pyridine N ‐oxides.
Cover Image (2020)

The cover image is based on the Original Article Consolidated bioprocessing performance of a two-species microbial consortium for butanol production from lignocellulosic biomass by Jiasheng Lu et al., https://doi.org/10.1002/bit.27464.
Real-time stereo tracking for head pose and gaze estimation (2002)

Computer systems which analyse human face/head motion have attracted significant attention recently as there are a number of interesting and useful applications. Not least among these is the goal of tracking the head in real time. A useful extension of this problem is to estimate the subject's gaze point in addition to his/her head pose. This paper describes a real-time stereo vision system which determines the head pose and gaze direction of a human subject. Its accuracy makes it useful for a number of applications including human/computer interaction, consumer research and ergonomic assessment.
The interaction between HLA shared epitope alleles and smoking and its contribution to autoimmunity against several citrullinated antigens (2011)

Our data indicate that the gene-environment interaction between HLA shared epitope alleles and smoking does not appear to shape the reactivity of the ACPA response. These data suggest that smoking promotes nonspecific citrullination rather than citrullination of specific antigens.
About yield surfaces of phase transformation for some shape memory alloys : duality and convexity. Application to fracture. Dynamical behavior of SMA (2008)

Juin
Genetic alterations of the KLF6 gene in colorectal cancers (2006)

To investigate whether the KLF6 gene plays an important role in the development and/or progression of colorectal cancers, we searched for mutations and allelic loss of the KLF6 gene in 123 colorectal adenocarcinomas by performing PCR-SSCP sequencing. We found five somatic missense mutations: S155N, G163S, G163D, P183L and G195S. Three of them affected the activation domain of KLF6 and four mutations were predicted to disrupt the putative phosphorylation sites. On LOH analysis, 63 cases were heterozygous for at least one marker and 27 cases (42.9%) showed allelic loss at these markers. These data further support that the KLF6 gene may be one of the candidate tumor suppressor genes in colorectal cancers and that genetic alteration of the KLF6 gene might play a role in the development of colorectal carcinomas.
Allostimulatory Effects of Dendritic Cells with Characteristic Features of a Regulatory Phenotype (2016)

LiClPAM3 DCs display in vitro a tolerogenic phenotype with a high IL-10:IL-12 ratio, but appeared to be highly immunogenic, since allograft rejection was accelerated. As yet unidentified LiClPAM3 DC-derived factors, may explain the immunogenic character of LiClPAM3 DCs in vivo.
New hopes from endophytic fungal secondary metabolites (2007)

The search for and exploitation of natural products and&#13;\ntheir properties has been the mainstay of biotechnology research. Natural product search and discovery from endophytes of medicinal plants represents a challenge to the biotechnologist. All the available evidence points to natural product discovery continuing strongly and &#13;\naccelerating as a consequence of new search strategies and innovative microbiology. In drug discovery, novel natural product chemotypes with interesting structures and biological activities continue to be reported. Without such discoveries, there would be a significant therapeutic deficit in several important clinical areas. The diverse range of biosynthetic pathways in plants, fungi and bacteria has provided an array of lead structures that have been used in drug development. This review highlights the importance of endophytes with desirable bioactivity, in a novel natural products screening programme.
Controlled microfluidic switching in arbitrary time-sequences with low drag (2013)

The ability to test the response of cells and proteins to a changing biochemical environment is of interest for studies of fundamental cell physiology and molecular interactions. In a common experimental scheme the cells or molecules of interest are attached to a surface and the composition of the surrounding fluid is changed. It is desirable to be able to switch several different biochemical reagents in any arbitrary order, and to keep the flow velocity low enough so that the cells and molecules remain attached and can be expected to retain their function. Here we develop a device with these capabilities, using U-shaped access channels. We use total-internal reflection fluorescence microscopy to characterize the time-dependent change in concentration during switching of solutions near the device surface. Well-defined fluid interfaces are formed in the immediate vicinity of the surface ensuring distinct switching events. We show that the experimental data agrees well with Taylor-Aris theory in its range of validity. In addition, we find that well-defined interfaces are achieved also in the immediate vicinity of the surface, where analytic approaches and numerical models become inaccurate. Assisted by finite-element modelling, the details of our device were designed for use with a specific artificial protein motor, but the key results are general and can be applied to a wide range of biochemical studies in which switching is important.
Low-power area-efficient high-speed I/O circuit techniques (2000)

We present a 4-Gb/s I/O circuit that fits in 0.1-mm/sup 2/ of die area, dissipates 90 mW of power, and operates over 1 m of 7-mil 0.5-oz PCB trace in a 0.25-/spl mu/m CMOS technology. Swing reduction is used in an input-multiplexed transmitter to provide most of the speed advantage of an output-multiplexed architecture with significantly lower power and area. A delay-locked loop (DLL) using a supply-regulated inverter delay line gives very low jitter at a fraction of the power of a source-coupled delay line-based DLL. Receiver capacitive offset trimming decreases the minimum resolvable swing to 8 mV, greatly reducing the transmission energy without affecting the performance of the receive amplifier. These circuit techniques enable a high level of I/O integration to relieve the pin bandwidth bottleneck of modern VLSI chips.