gebhart/patrepeval huggingface dataset:
A multi-microchip retinal stimulator for in vitro / in vivo experiments (2007)

This paper describes the fabrication and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vitro</i> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> operation of a retinal stimulator based on CMOS multi-microchips. To enhance reliability and reproducibility for <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vitro</i> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> with large array size, we introduce a flip-chip bonding technique and place microchips on the reverse side of a substrate. A microchip with a size of 600 mum square was fabricated using 0.35- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> m standard CMOS process technology. Twelve microchips were flip-chip bonded on a polyimide substrate through Au bumps. We successfully fabricated a stimulator with 12 microchips and 118 electrodes made of Pt/Au bumps. For <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vitro</i> , we demonstrated their operation in a saline solution over two weeks. Also, for <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> , a stimulator with one active IrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&#x01d4cd;</sub> electrode was implanted into the scleral pocket of a rabbit and EEP signals with a threshold of 100 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> A were obtained.
Table S1 from Phase I Dose-Escalation and -Expansion Study of Telisotuzumab (ABT-700), an Anti–c-Met Antibody, in Patients with Advanced Solid Tumors (2023)

&lt;p&gt;Additional details for TEAEs and TRAEs for all doses in the escalation cohort&lt;/p&gt;
1723 Diagnostic accuracy of a novel transcriptomic classifier for bacterial and viral infections – an individual patient data meta-analysis (2022)

Aims, Objectives and Background Arising from demographic differences between healthcare systems, patients in the emergency department (ED) present with a broad range of diagnoses and clinical severities. Independent validation of a novel diagnostic tool is critical to ensure reliable and reproducible clinical performance. So far, three independent cohort studies have validated the performance of the machine-learning classifier IMX-Bacterial/Viral/Non-infected (IMX-BVN) to diagnose bacterial and viral infections; those have been combined to facilitate an individual patient data meta-analysis of performance. Method and Design ED patients (n=1,277) with suspected infection from three international, observational studies (USA/Germany/Greece) were included. Of those, 661 had a unanimous (‘consensus’) ground truth of infection status established by panel adjudication. Quantitative expression of 29-signature mRNAs was measured on a NanoString nCounter® SPRINT system. The classifier BVN version 3 (IMX-BVN-3) was applied to generate scores, which fall into four discrete interpretation bands (very unlikely, unlikely, possible, very likely). Sensitivity, specificity, and corresponding nominal likelihood ratios were calculated with 95% confidence intervals for each interpretation band. Results and Conclusion 360 patients (54.4%) were consensus adjudicated to have a bacterial infection (range: 37.9–81.2%) and 153 (23.1%) to have a viral infection (range: 15.3–44.1%). Pooled likelihood ratios of the interpretation bands for bacterial infections were (from ‘very unlikely bacterial’ to ‘very likely bacterial’) 0.082 (0.039–0.176)/0.333 (0.264–0.419)/2.244 (1.598–3.152)/9.459 (5.808–15.404), associated with a rule-in specificity of 0.947 (0.915–0.967) and a rule-out sensitivity of 0.981 (0.960–0.991) in the outer interpretation bands. Pooled likelihood ratios of the interpretation bands for viral infections were (from ‘very unlikely viral’ to ‘very likely viral’) 0.182 (0.102–0.324)/0.292 (0.181–0.471)/0.956 (0.593–1.540)/6.021 (4.636–7.821), associated with a rule-in specificity of 0.884 (0.853–0.909) and rule-out sensitivity of 0.928 (0.876–0.959). The IMX-BVN-3 classifier exhibits strong performance in a combined cohort of patients from different geographies and settings to rule-in and rule-out patients presenting to EDs with suspected bacterial and viral infections.
System for remote multi-channel real-time monitoring of ECG via the internet (2005)

Continuous physiological data monitoring of subjects has heretofore required the researcher to be in immediate proximity to the subject. Such 'bedside monitoring' is impractical in long-term studies, as often the subject and research facilities are in geographically disparate locations. Another limitation of existing technologies prohibits long-term data archiving without substantial user intervention. We constructed a novel hardware and software platform allowing us to visualize, via the Internet, encrypted real-time ECG signals from mice used in preclinical cardiovascular studies. As the design is highly modular, it can easily be adapted for use on different subjects and/or different signals of interest. The hardware consists of analog signal-conditioning PCBs (schematics on Physionet) and an A/D board with open-source APIs for digitizing data. In its current incarnation, the system simultaneously monitors ECGs of 16 mice with implanted electrodes, streaming the data to the network for remote visualization and to a RAID partition on the acquisition server for archiving purposes. As the mouse heart rate is roughly 10 times that of a human, the processing power and network bandwidth required of the system is equivalent to that needed to monitor 160 humans simultaneously. The system can collect data on multiple mice, with no user intervention, for months at a time. Data acquisition is controlled through an intuitive web interface that permits simple starting and stopping of acquisition while requiring the user to enter dam into a customizable HTML record that is written to an SQL database for accurate record-keeping. In the past 8 months we have collected and analyzed more data, with far less effort, than the formerly-used commercial system allowed in over two years. The remote visualization capability of our system has provided us unprecedented intuition and insight into long-term trends of cardiovascular disease of pre-clinical subjects. The database-driven web record entry has provided a paperless environment, replacing extensive manual logbook entries that once prevailed prior to long-term data collection capabilities.
Controllable Image Illumination Enhancement with an Over-Enhancement Measure (2018)

The quality of images or videos that suffer from exposure distortions can be enhanced using histogram equalization or retinex methods. However, the relationship between the visual quality and the degree of enhancement is an inverted U-shaped function with a peak point, and many existing methods have parameters that have no clear relationship with image quality. We introduce a controllable illumination enhancement system, where the degree of enhancement can be adjusted using a single parameter. We then propose an over-enhancement measure, Lightness Order Measure (LOM), which quantifies the unnaturalness based on a local inversion of lightness order. We explore the relationship between the peak point and LOM in a subjective test. The results indicate that LOM reduces content dependency compared to existing methods. Our subjective test also evaluates the image quality of our enhancement, and demonstrates the effectiveness of our method.
Arbitrary optical short pulse generator using a high-resolution arrayed-waveguide grating (2005)

We demonstrate an arbitrary optical short pulse generator using a high-resolution arrayed-waveguide grating with integrated 30-ch amplitude/phase modulators. The Gaussian pulse with a repetition rate of 10 GHz is successfully generated at various center frequencies.
Improvement of electron emission efficiency and stability by surface application of molybdenum silicide onto gated poly-Si field emitters (1998)

As an approach to improve electron field emission and its stability, molybdenum (Mo) silicide formation on n/sup +/ polycrystalline silicon (poly-Si) emitters has been investigated. Mo silicide was produced by direct metallurgical reaction, namely, deposition of Mo and subsequent rapid thermal annealing. The surface morphologies and emission properties of Mo-silicided poly-Si (Mo-polycide) emitters have been examined and compared with those of poly-Si emitters. While anode current of 0.1 μA per tip could be obtained at the gate voltage of 82 V from poly-Si emitters, the same current level was measured at 72 V from Mo-polycide emitters. In addition, the application of Mo silicide onto poly-Si emitters reduced the emission current fluctuation considerably. These results show that the polycide emitters can have potential applications in vacuum microelectronics to obtain superior electron emission efficiency and stability.
Suppression of autophagy by FIP200 deletion leads to osteopenia in mice through the inhibition of osteoblast terminal differentiation (2013)

Autophagy is a conserved lysosomal degradation process that has important roles in both normal human physiology and disease. However, the function of autophagy in bone homeostasis is not well understood. Here, we report that autophagy is activated during osteoblast differentiation. Ablation of focal adhesion kinase family interacting protein of 200 kD (FIP200), an essential component of mammalian autophagy, led to multiple autophagic defects in osteoblasts including aberrantly increased p62 expression, deficient LC3-II conversion, defective autophagy flux, absence of GFP-LC3 puncta in FIP200-null osteoblasts expressing transgenic GFP-LC3, and absence of autophagosome-like structures by electron microscope examination. Osteoblast-specific deletion of FIP200 led to osteopenia in mice. Histomorphometric analysis revealed that the osteopenia was the result of cell-autonomous effects of FIP200 deletion on osteoblasts. FIP200 deletion led to defective osteoblast terminal differentiation in both primary bone marrow and calvarial osteoblasts in vitro. Interestingly, both proliferation and differentiation were not adversely affected by FIP200 deletion in early cultures. However, FIP200 deletion led to defective osteoblast nodule formation after initial proliferation and differentiation. Furthermore, treatment with autophagy inhibitors recapitulated the effects of FIP200 deletion on osteoblast differentiation. Taken together, these data identify FIP200 as an important regulator of bone development and reveal a novel role of autophagy in osteoblast function through its positive role in supporting osteoblast nodule formation and differentiation.
Optogenetic stimulation of cholinergic brainstem neurons during focal limbic seizures: Effects on cortical physiology (2015)

Focal temporal lobe seizures often cause impaired cortical function and loss of consciousness. Recent work suggests that the mechanism for depressed cortical function during focal seizures may depend on decreased subcortical cholinergic arousal, which leads to a sleep-like state of cortical slow-wave activity. To test this hypothesis, we sought to directly activate subcortical cholinergic neurons during focal limbic seizures to determine the effects on cortical function. Here we used an optogenetic approach to selectively stimulate cholinergic brainstem neurons in the pedunculopontine tegmental nucleus during focal limbic seizures induced in a lightly anesthetized rat model. We found an increase in cortical gamma activity and a decrease in delta activity in response to cholinergic stimulation. These findings support the mechanistic role of reduced subcortical cholinergic arousal in causing cortical dysfunction during seizures. Through further work, electrical or optogenetic stimulation of subcortical arousal networks may ultimately lead to new treatments aimed at preventing cortical dysfunction during seizures.
ChemInform Abstract: Complexes of N‐Heterocyclic Carbenes (2001)

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.
Kinetic Stress Testing and the Influence of Long-Time Anneals on the Behavior of IZO Thin Film Transistors (2013)

Stability testing of indium-zinc oxide under extreme conditions is necessary before the metal oxide can be deemed a reliable alternative to a-Si as channel layer in thin film transistors (TFTs). In this paper, we apply thermal stress under positive and negative gate bias stress creating practical application conditions. This stress scenario gives greater insight into thermally activated defects in the presence of an electrical field. Operational temperatures of 20 °C, 50 °C, and 80 °C are used, and a more rapid degradation of the devices is seen with increased temperatures. Kink and dip are observed due to the donor-like trapped charges increasing the subthreshold swing and acceptor-like trapped charges reducing the ON current, respectively. Post fabrication, long-time anneals for 12-, 24-, 36-, 48-, and 60-h at low temperatures (150 °C) are performed to alleviate defects. The 48-h annealed TFTs show remarkable stability under extreme temperatures and electric fields maintaining a high ON-OFF ratio (~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> ) after 104 s. This is attributed to the reduced density of charges in acceptor-like trap states, modeled to reduce by 58% from a 12-h anneal and to insignificant extent over a 48-h anneal.
A Long-Circulating co-Polymer in “Passive Targeting” to Solid Tumors (1997)

A co-polymer of O-methyl polyethylene(glycol)-O'-succinate (MPEGs, m.w. 5100) and poly-l-lysine (PL, median m.w. 32700, degree of polymerization 256) has been synthesized by covalent grafting. The resultant MPEGs-PL (30% modification degree of epsilon-amino groups) had a hydrodynamic diameter corresponding to a 690 kD protein. Free amino groups (180/mol of the co-polymer) were used for conjugation of diethylene pentaacetic or succinic acid residues to MPEGs-PL. The potential of the resultant compound as a carrier of therapeutic and diagnostic drugs was studied using a rodent carcinoma models. The co-polymer had a blood pool half-life of 36h in adenocarcinoma-bearing rats. Radioactively labeled preparations were resistant to trans-chelation with apotransferrin and stable in blood for 24 h. The co-polymer accumulated in solid tumors at the level of 1.5-2% injected dose/g of tumor in 24 h. At that time, 34-40% of the accumulated polymer was associated with tumor cell fraction. The co-polymer non-covalently associated with cis-diamminedichloroplatinum(II), showed a cytostatic effect against mouse F9 carcinoma, and induced a reversal in tumor growth after intravenous administration.
Different Modes of Action of the Imidazoline Compound RX871024 in Pancreatic β‐Cells: Blocking of K+ Channels, Mobilization of Ca2+ from Endoplasmic Reticulum, and Interaction with Exocytotic Machinerya (1999)

The imidazoline compound RX871024 glucose-dependently potentiates the release of insulin in pancreatic islets and beta-cell lines. This activity of the compound is not related to its action by stimulating alpha 2-adrenoceptors and I1- and I2-imidazoline receptors. There are at least three modes of action of RX871024 in beta-cells: (1) RX871024 blocks the ATP-dependent, Ca(2+)-activated, and delayed rectifier K+ channel activity; (2) RX871024 causes mobilization of Ca2+ from thapsigargin-sensitive intracellular stores, the effect probably controlled by cytochrome P450; and (3) the stimulatory activity of RX871024 on insulin release involves interaction of the compound with the exocytotic machinery, unrelated to the changes in membrane potential and cytoplasmic-free Ca2+ concentration, whereas protein phosphorylation plays an important role in this process. The maximal insulinotropic effect of RX871024 is much higher than that of the sulfonylurea glibenclamide. RX871024 stimulates insulin release and normalizes blood glucose levels in rats in vivo without affecting blood pressure and heart rate.
Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment (2020)

Mycobacterium tuberculosis and M. smegmatis form drug-tolerant biofilms through dedicated genetic programs. In support of a stepwise process regulating biofilm production in mycobacteria, it was shown elsewhere that lsr2 participates in intercellular aggregation, while groEL1 was required for biofilm maturation in M. smegmatis. Here, by means of RNA-Seq, we monitored the early steps of biofilm production in M. bovis BCG, to distinguish intercellular aggregation from attachment to a surface. Genes encoding for the transcriptional regulators dosR and BCG0114 (Rv0081) were significantly regulated and responded differently to intercellular aggregation and surface attachment. Moreover, a M. tuberculosis H37Rv deletion mutant in the Rv3134c-dosS-dosR regulon, formed less biofilm than wild type M. tuberculosis, a phenotype reverted upon reintroduction of this operon into the mutant. Combining RT-qPCR with microbiological assays (colony and surface pellicle morphologies, biofilm quantification, Ziehl-Neelsen staining, growth curve and replication of planktonic cells), we found that BCG0642c affected biofilm production and replication of planktonic BCG, whereas ethR affected only phenotypes linked to planktonic cells despite its downregulation at the intercellular aggregation step. Our results provide evidence for a stage-dependent expression of genes that contribute to biofilm production in slow-growing mycobacteria.
APPLICATION OF GEOTEXTILES FOR THE STABILIZATION OF STEEP SLOPES IN GRAVEL PITS (2017)

Innovative geotextiles formed from meandrically arranged ropes were used for the protection of the steep slope in the gravel pit Nieboczowy. The geotextiles from textile wastes were produced. Segments of geotextiles were mounted on the slope in winter. After installing for six months the slope condition was monitored. It was found that immediately after installation the geotextiles prevent the ground sliding. Ropes laterally arranged on the slope absorb significant amounts of water and create microdam system, which slow down a runoff. In spring the geotextiles accelerate the development of vegetation. Lush vegetation covering the entire surface of the slope supports the stabilizing effect of geotextiles. Geotextiles effectively protect the embankment against landslides and the consequences of surface erosion. Geotextiles can be successfully applied in the process of reclamation of disused gravel pits.
Effect of Amino Acids on the Nitrogenase System of Klebsiella pneumoniae (1966)

Yoch, D. C. (South Dakota State University, Brookings), and R. M. Pengra. Effect of amino acids on the nitrogenase system of Klebsiella pneumoniae. J. Bacteriol. 92:618-622. 1966.-The effect of exogenous amino acids and the free amino acid pool on the synthesis of the nitrogenase system of Klebsiella pneumoniae M5al (formerly Aerobacter aerogenes M5al) was investigated. When an actively N(2)-fixing culture was used to inoculate a medium containing a limiting concentration of NH(4) (+), an induction lag period was observed. When either a single amino acid or a mixture of amino acids was substituted at the same nitrogen concentration, growth was uninterrupted by the induction period. It appears that a step or steps in the formation of the nitrogenase system are repressed by NH(4) (+) and are not affected by amino acid N. The amino acids, far from repressing formation of nitrogenase as does NH(4) (+), actually stimulate its formation. It appears that both free and amino nitrogen are used simultaneously. The amino acids that served concomitantly with N(2) as a source of nitrogen were: aspartic acid, serine, threonine, leucine, and histidine. Of these amino acids, it was shown that aspartic acid is readily taken up by the cells. Of the amino acids not serving as an immediate nitrogen source, isoleucine is not taken up by the cells. The free amino acid pool of the cells was measured at the onset and termination of the induction period. Ninhydrin-positive material in the amino acid pool was depleted by 35% during the induction period.
Enantioselective Hydrogenation of N-H Imines (2009)

A) Preparation and Physical Data for N-H imines Hydrochloride S1 (B) General Procedure for Asymmetric Hydrogenation of N-H imines Hydrochloride .. ..S6 (C) Analytical Data for the Hydrogenation Products . S6 (D) Imine Deuteration experiment...S11 (E) NMR Spectra of new products .. ...S12 (F) GC Charts for Hydrogenation Products ......S25 General: Unless otherwise noted all reactions were run under a nitrogen atmosphere, solvents and reagents were transferred by syringe. All manipulations involving [Ir(COD)Cl] 2 and (S,S)-f-binaphane were performed in a N 2 -filled glove-box. NMR spectra were recorded with a Varian spectrometer at 400 MHz ( 1 H NMR) and 100 MHz ( 13 C NMR) or 500 MHz ( 1 H NMR) and 125 MHz ( 13 C NMR) in CD 3 OD, DMSO-d 6 or CDCl 3 . Chemical shifts were reported in ppm downfield from internal Me 4 Si. Optical rotations were determined using a Perkin Elmer 341 MC polarimeter. HRMS were recorded on a Thermo LTQ Orbitrap hybrid mass spectrometer.
ChemInform Abstract: Mild Acetalization of Mono and Dicarbonyl Compounds Catalyzed by Titanium Tetrachloride. Facile Synthesis of β‐Keto Enol Ethers. (2001)

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.