gebhart/patrepeval huggingface dataset:
Role of spectral counting in quantitative proteomics (2010)

Spectral count, defined as the total number of spectra identified for a protein, has gained acceptance as a practical, label-free, semiquantitative measure of protein abundance in proteomic studies. In this review, we discuss issues affecting the performance of spectral counting relative to other label-free methods, as well as its limitations. Possible consequences of modifications, which are commonly applied to raw spectral counts to improve abundance estimations, are considered. The use of spectral counting for different types of quantitation studies is explored and critiqued. Different statistical methods and underlying frameworks that have been applied to spectral count analysis are described and compared, and problem areas that undermine confident statistical analysis are considered. Finally, the issue of accurate estimation of false-discovery rates is addressed and identified as a major current challenge in quantitative proteomics.
A/T/N: An unbiased descriptive classification scheme for Alzheimer disease biomarkers (2016)

Biomarkers have become an essential component of Alzheimer disease (AD) research and because of the pervasiveness of AD pathology in the elderly, the same biomarkers are used in cognitive aging research. A number of current issues suggest that an unbiased descriptive classification scheme for these biomarkers would be useful. We propose the "A/T/N" system in which 7 major AD biomarkers are divided into 3 binary categories based on the nature of the pathophysiology that each measures. "A" refers to the value of a β-amyloid biomarker (amyloid PET or CSF Aβ42); "T," the value of a tau biomarker (CSF phospho tau, or tau PET); and "N," biomarkers of neurodegeneration or neuronal injury ([(18)F]-fluorodeoxyglucose-PET, structural MRI, or CSF total tau). Each biomarker category is rated as positive or negative. An individual score might appear as A+/T+/N-, or A+/T-/N-, etc. The A/T/N system includes the new modality tau PET. It is agnostic to the temporal ordering of mechanisms underlying AD pathogenesis. It includes all individuals in any population regardless of the mix of biomarker findings and therefore is suited to population studies of cognitive aging. It does not specify disease labels and thus is not a diagnostic classification system. It is a descriptive system for categorizing multidomain biomarker findings at the individual person level in a format that is easy to understand and use. Given the present lack of consensus among AD specialists on terminology across the clinically normal to dementia spectrum, a biomarker classification scheme will have broadest acceptance if it is independent from any one clinically defined diagnostic scheme.
The influence of deep (odontogenic) pain intensity, quality, and duration on the incidence and characteristics of referred orofacial pain. (1996)

This study examined the effects of the intensity, quality, and duration of odotogenic pain on the incidence, pattern, and clinical characteristics of pain referral in the orofacial region. Four hundred consecutive patients reporting with posterior toothache to the dental emergency clinic were included. Patients completed a standardized clinical questionnaire consisting of a numerical rating scale for pain intensity and chose verbal descriptors from a list of adjectives describing the quality of their pain. In addition, patients indicated sites to which pain referred by drawing on a mannequin* of the head and neck. Pain intensity was found to significantly affect the presence of referred pain (P < .005). However, neither duration nor quality of pain influenced the incidence of referred pain. Finally, pain referral occurred in vertical laminations as indicated on mannequin drawings, but these were not found to be diagnostic because of extensive horizontal overlap. The association of intensity and referral is attributed to central nervous system hyperexitability causing expansion of receptive fields and spread and referral of pain.
Phenolic Compounds from Artichoke (Cynara scolymus L.) By-products and their Antimicrobial Activities (2013)

Cynara scolymus L. is a medicinal plant frequently used in traditional medicine for liver diseases. The aim of this study is to evaluate the antimicrobial activity of the different parts of Artichoke. Maximum antimicrobial activity was observed with methanolic extract of bound phenols for (bract and heart) against Gram negative bacteria. The MIC values for bound phenols from heart were (63?g/ml). Whereas, the bound phenols for bracts was ranged from (312 and 486?g/ml) against Gram negative and (486?g/ml) against Gram positive. Free phenols of the heart of artichoke showed the lowest MIC (204 to 206) ?g/mL for microorganism Gram positive and Gram negative. Therefore, this study indicate that the free phenolic extract from bracts of Cynara scolymus L . might be of interest within the developing market of nutritional ingredients and is capable of yielding nutritional supplements with antimicrobial activities. Key words: artichoke wastes, antibacterial effects
Interinstitutional and interstate teleneuropathology (2011)

Lessons learned from this successful venture can be used to facilitate future efforts in this ever-growing practical vehicle for distributing pathology subspecialty expertise.
Modular pixelated detector system with the spectroscopic capability and fast parallel read-out (2014)

A modular pixelated detector system was developed for imaging applications, where spectroscopic analysis of detected particles is advantageous e.g. for energy sensitive X-ray radiography, fluorescent and high resolution neutron imaging etc. The presented system consists of an arbitrary number of independent versatile modules. Each module is equipped with pixelated edgeless detector with spectroscopic ability and has its own fast read-out electronics. Design of the modules allows assembly of various planar and stacked detector configurations, to enlarge active area or/and to improve detection efficiency, while each detector is read-out separately. Consequently read-out speed is almost the same as that for a single module (up to 850 fps). The system performance and application examples are presented.
Destruction of living cells by pulsed high-voltage application (1988)

Destruction of living cells in liquid has been formed by pulsed high-voltage application to the liquid. S. cerevsaie (yeast cell) or Bacillus natto, dispersed in deionized water and one- and three-percent NaCl solution, were used in this experiment. Four different electrodes (plate-plate, needle-plate wire-cylinder, and rod-rod electrode) were tested. The survival rate of cells was measured against peak electric field E/sub p/ pulsewidth T/sub W/, and pulse application number N. The experimental results indicate that the survivability roughly follows Weilbull distribution. Yeast cells dispersed in deionized water could be almost completely destroyed when the wire-cylinder electrode was used with E/sub p/=20 kV/cm, T/sub W/=100 mu s, and N=200. The energy input to a unit volume of the liquid to complete the cell destruction, however, differed significantly with the electrode type. The wire-cylinder electrode required above 10-30 cal/cm/sup 3/ to destroy the yeast cell in deionized water to 10/sup -6/ survivability. This value was less than that required more than 70 cal/cm/sup 3/. Using the rod-rod electrode contained in a pressure vessel, an arc discharge was generated to produce an intensive shock wave, which also destroyed the cells by its mechanical force. In this case, 5-10 cal/cm/sup 3/ of energy was required to decrease the survivability of yeast cells in deionized water to 10/sup -6/. Though further studies are necessary, this results indicate a possibility of the cell destruction by pulsed high voltage to be used as an energy-efficient sterilization process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The implementation of distributed high-speed high-accuracy data acquisition system based on EtherCAT (2013)

In order to overcome the limitation of traditional data-acquisition card based on PCI bus, a novel data-acquisition system featuring high-speed and high-accuracy is implemented based on real-time industrial internet technology EtherCAT(Ethernet for Control Automation Technology). Without the requirement of a dedicated hardware card of IPC(Industrial PC), such kind of data acquisition system can be connected with IPC using the normal NIC card, hence the whole cost is reduced. Up to 65535 such devices can be connected to form a distributed data-acquisition which enables the possibilities of acquiring data distributed in large-scale areas. In addition, with the help of FPGA and DSP, the data converted from ADC can be processed such as filtered and compressed before transmitted to IPC, which reduces the processing load of IPC and in turn increases the overall system performance.
The Chemistry of the quinonoid compounds (1974)

This is Part 2 of the second volume of a three volume work devoted to the chemistry of quinonoid compounds. Part 1 is published simultaneously, as is a volume set containing both parts. The work is intended to form a comprehensive review of the current state of research in quinonoid compounds starting with general and theoretical aspects and encompassing, among other things, physical and chemical methods, mass spectra, PES, chiroptical properties, chemiluminescence, recent advances in the synthesis of quinonoid compounds and in photochemistry, chemistry and biochemistry.
Creatine supplementation with specific view to exercise/sports performance: an update (2012)

Creatine is one of the most popular and widely researched natural supplements. The majority of studies have focused on the effects of creatine monohydrate on performance and health; however, many other forms of creatine exist and are commercially available in the sports nutrition/supplement market. Regardless of the form, supplementation with creatine has regularly shown to increase strength, fat free mass, and muscle morphology with concurrent heavy resistance training more than resistance training alone. Creatine may be of benefit in other modes of exercise such as high-intensity sprints or endurance training. However, it appears that the effects of creatine diminish as the length of time spent exercising increases. Even though not all individuals respond similarly to creatine supplementation, it is generally accepted that its supplementation increases creatine storage and promotes a faster regeneration of adenosine triphosphate between high intensity exercises. These improved outcomes will increase performance and promote greater training adaptations. More recent research suggests that creatine supplementation in amounts of 0.1 g/kg of body weight combined with resistance training improves training adaptations at a cellular and sub-cellular level. Finally, although presently ingesting creatine as an oral supplement is considered safe and ethical, the perception of safety cannot be guaranteed, especially when administered for long period of time to different populations (athletes, sedentary, patient, active, young or elderly).
Interferon Induction in Rabbit Cells Irradiated with UV Light (1974)

UV irradiation of a continuous line of rabbit kidney cells (RK13) was used as a tool for the study of the mechanism of interferon induction. Irradiation of cells prior to their exposure to Newcastle disease virus (NDV) resulted in a dose-dependent decrease in interferon production. The inhibition of total cellular RNA synthesis by UV irradiation in uninduced cultures was similar to the inactivation curve of interferon production in NDV-induced cultures. In contrast, the production of interferon with polyinosinate-polycytidylate (poly[I].poly [C]) paradoxically was enhanced in cells irradiated with a wide range of doses of UV. However, in cells stimulated with poly(I).poly(C) and "superinduced" by the sequential addition of cycloheximide and actinomycin D, the rate of inactivation of interferon production by UV light was similar to that observed with NDV. These results are not inconsistent with the idea that both poly(I).poly(C) and NDV stimulate the same interferon gene(s), but indicate that the mechanism controlling its expression may be different for each inducer.
Theory of Electron-Transfer Reactions and of Related Phenomena (1965)

Data on electron exchange reactions have provided insight into factors influencing rates of electron-transfer reactions in solution. The present paper has the twofold purpose of discussing some of these factors and of describing applications of these exchange data and theory to other phenomena. The reaction rate depends upon the extent of reorganization of bond lengths (angles) in the reactants and of solvent reorientation outside them. The reorganization is facilitated or hindered in a comparatively simple way by a favorable or unfavorable standard free energy of reaction. The rate depends, too, on coulombic and other interactions, as evidenced perhaps by certain salt effects, though probably only by a few orders of magnitude typically. The observed variation of rates of some 15 orders of magnitude is best attributed primarily 10\ndifferences in the vibrational reorganization term, a factor calculable from bond lengths and force constants\nwhen known. A remaining factor, non-adiabaticity, is at present of uncertain importance. Arrhenius frequency\nfactors in chemical and electrochemical exchange rate constants would provide the most direct information,\nbut can be complicated or even dwarfed by solvent reordering effects in the coulombic interaction. Available\ndata are few. They provide examples where a non-adiabatic effect is minor. There appear to be no known examples where it is major (Fe2+ - Fe3+ could be a candidate but its mechanism is apparently uncertain). Reorganization in reactants and in solvent occurs in a variety of related phenomena, and related concepts will be applied to treat them. In turn, chemical exchange data have useful applications to the latter. These areas include electrochemical exchange reactions, chemiluminescent electron-transfer reactions (between positive and negative aromatic ions, for example), and redox reactions of the solvated electron. An explanation for the chemiluminescent reactions will be based on the possible "inverse ΔF" effect, discussed several years ago by the author. A related phenomenon involving solvent "orientation strain" occurs in light absorption or emission by polar solutes in polar solvents, and the theoretical approach used by the author for treating it is closely related to that used for the exchange reactions.
MVSCRF: Learning Multi-View Stereo With Conditional Random Fields (2019)

We present a deep-learning architecture for multi-view stereo with conditional random fields (MVSCRF). Given an arbitrary number of input images, we first use a U-shape neural network to extract deep features incorporating both global and local information, and then build a 3D cost volume for the reference camera. Unlike previous learning based methods, we explicitly constraint the smoothness of depth maps by using conditional random fields (CRFs) after the stage of cost volume regularization. The CRFs module is implemented as recurrent neural networks so that the whole pipeline can be trained end-to-end. Our results show that the proposed pipeline outperforms previous state-of-the-arts on large-scale DTU dataset. We also achieve comparable results with state-of-the-art learning based methods on outdoor Tanks and Temples dataset without fine-tuning, which demonstrates our method's generalization ability.
Simvastatin and purine analogs have a synergic effect on apoptosis of chronic lymphocytic leukemia cells (2010)

Despite many therapeutic regimens introduced recently, chronic lymphocytic leukemia (CLL) is still an incurable disorder. Thus, there is an urgent need to discover novel, less toxic and more effective drugs for CLL patients. In this study, we attempted to assess simvastatin, widely used as a cholesterol-lowering drug, both as a single agent and in combination with purine analogs-fludarabine and cladribine-in terms of its effect on apoptosis and DNA damage of CLL cells. The experiments were done in ex vivo short-term cell cultures of blood and bone marrow cells from newly diagnosed untreated patients. We analyzed expression of active caspase-3 and the BCL-2/BAX ratio as markers of apoptosis and the expression of phosphorylated histone H2AX (named γH2AX) and activated ATM kinase (ataxia telangiectasia mutated kinase), reporters of DNA damage. Results of our study revealed that simvastatin induced apoptosis of CLL cells concurrently with lowering of BCL-2/BAX ratio, and its pro-apoptotic effect is tumor-specific, not affecting normal lymphocytes. We observed that combinations of simvastatin+fludarabine and simvastatin+cladribine had a synergic effect in inducing apoptosis. Interestingly, the rate of apoptosis caused by simvastatin alone and in combination was independent of markers of disease progression like ZAP-70 and CD38 expression or clinical stage according to Rai classification. We have also seen an increase in γH2AX expression in parallel with activation of ATM in most of the analyzed samples. The results suggest that simvastatin can be used in the treatment of CLL patients as a single agent as well as in combination with purine analogs, being equally effective both in high-risk and good-prognosis patients. One of the mechanisms of simvastatin action is inducing DNA damage that ultimately leads to apoptosis.
Fluorous Mixture Synthesis of (−)-Dictyostatin and Three Stereoisomers (2005)

[reaction: see text] A mixture of four stereoisomers whose configurations are encoded by fluorous silyl protecting groups has been prepared and converted over 22 steps to a mixture of protected dictyostatins. Demixing by fluorous HPLC followed by removal of the fluorous protecting groups (detagging) provides dictyostatin and three C6,C7 stereoisomers. Biological evaluation showed that the monoepimers of the natural product retained highly potent activity.
Spatio-temporal phase-encoding profilometry using correlation image sensor (2008)

In this paper, we propose a real-time 3D shape measurement system which consists of 1) a moving fringe projector for spatio-temporal encoding (single frequency in time but different phase in space) of illumination angle, and 2) the three-phase correlation image sensor (3PCIS) which performs the synchronous detection and amplitude/phase demodulation of intensity-modulated light in real time on each pixel. The 3PCIS demodulates amplitude and phase of moving fringes in a scene frame by frame. Then, it is unwrapped in real-time to a sequence of projection angle maps based on an efficient use of spatial and temporal continuity of the phase maps. Compared with the phase-shift method using a color image sensor or a high speed camera, the system is shown to have novel characteristics; pixel by pixel capture of phase map in a single frame, freedom from environmental light sources and grayness nonlinearity of fringes, reduced sensitivity to object motion, etc. We implemented this system using CMOS 200times200 and 320times256 pixel 3PCIS recently developed by us.
High-speed CMOS circuit technique (1989)

It is shown that clock frequencies in excess of 200 MHz are feasible in a 3- mu m CMOS process. This performance can be obtained by means of clocking strategy, device sizing, and logic style selection. A precharge technique with a true single-phase clock, which increases the clock frequency and reduces the skew problems, is used. Device sizing with the help of an optimizing program improves circuit speed by a factor of 1.5-1.8. The logic depth is minimized to one instead of two or more, and pipeline structures are used wherever possible. Experimental results for several circuits which work at clock frequencies of 200-230 MHz are presented. SPICE simulation shows that some circuits could work up to 400-500 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Identification of C-terminal extensions that protect proteins from intracellular proteolysis (1989)

Revertants of defective mutants in the Arc repressor of bacteriophage P22 were isolated. Five of the six reverting mutations were frameshifts near the end of the coding sequence which resulted in proteins with C-terminal extensions. Each of the reverting mutations prolong the half-lives in vivo of the proteins in which they reside, yet they do not alter the thermodynamic stability, structure, oligomeric form, or DNA-binding properties of these proteins. Fusion of one of these tails to the C-terminal end of a mutant form of the N-terminal domain of lambda repressor also prevented proteolysis of this protein. These C-terminal sequences may prevent degradation by blocking the recognition of unstable proteins by the proteolytic machinery in the cell.
Electrochemical Er doping of porous silicon and its room-temperature luminescence at ∼1.54 μm (1994)

We present a new electro-chemical method for incorporating high concentration Er ions deep into porous silicon layers and its intense photoluminescence at ∼1.54 μm at room temperature. Porous silicon layers prepared by anodic etching of p-type silicon substrates in HF/H2O are immersed in ErCl3/ethanol solution. Then the negative bias relative to a counter platinum electrode is applied to the samples. Er3+ ions are drawn into fine pores of the porous silicon layers by the electric field. After thermal annealing at ∼1300 °C in an O2/Ar atmosphere, the samples show sharp and intense Er3+-related photoluminescence at ∼1.54 μm at room temperature upon excitation with an Ar ion laser.
Loss of T Regulatory Cell Suppression following Signaling through Glucocorticoid-induced Tumor Necrosis Receptor (GITR) Is Dependent on c-Jun N-terminal Kinase Activation (2012)

Naturally occurring Foxp3(+)CD4(+)CD25(+) T regulatory cell (nTreg)-mediated suppression of lung allergic responses is abrogated following ligation of glucocorticoid-induced tumor necrosis receptor (GITR) family-related protein. In vitro stimulation of nTregs with GITR ligand increased phosphorylation of c-Jun N-terminal kinase (JNK) but not extracellular signal-regulated protein kinase (ERK) or p38 MAPK. SP600125, a known JNK inhibitor, prevented GITR-mediated phosphorylation of JNK. Activation of JNK was associated with increases in the upstream mitogen-activated protein kinase kinase 7 (MKK7) and the downstream transcription factor NF-κβ. Phosphorylated c-Jun (p-c-Jun), indicative of the activation of JNK, was detected in the immunoprecipitates of nTregs from wild-type but not JNK- or GITR-deficient mice. Treatment with an inhibitor of JNK phosphorylation resulted in complete reversal of all GITR-induced changes in nTreg phenotype and function, with full restoration of suppression of in vivo lung allergic responses and in vitro proliferation of activated CD4(+)CD25(-) T cells. Thus, regulation of JNK phosphorylation plays a central role in T regulatory cell function with therapeutic implications for the treatment of asthma and autoimmune diseases.