gebhart/patrepeval huggingface dataset:
Efficient and optimal binary Hopfield associative memory storage using minimum probability flow (2012)

We present an algorithm to store binary memories in a Hopfield neural network using minimum probability flow, a recent technique to fit parameters in energy-based probabilistic models. In the case of memories without noise, our algorithm provably achieves optimal pattern storage (which we show is at least one pattern per neuron) and outperforms classical methods both in speed and memory recovery. Moreover, when trained on noisy or corrupted versions of a fixed set of binary patterns, our algorithm finds networks which correctly store the originals. We also demonstrate this finding visually with the unsupervised storage and clean-up of large binary fingerprint images from significantly corrupted samples.
Aortic Input Impedance Increases With Age in Healthy Men and Women (2005)

Aortic input impedance represents the hydraulic load presented by the systemic circulation to the left ventricle of the heart and is increased in patients with cardiovascular disease. Aging is a strong independent risk factor for cardiovascular disease and could exert this effect partly through an increase in modulus of aortic input impedance. We used a novel noninvasive technique to determine aortic input impedance in 71 healthy men and women aged 20 to 69 years. We found that the aortic input impedance spectrum was shifted rightward with advancing age, characterized by a 37% increase in the frequency of the minimum modulus between the third and seventh decade (P<0.0001). The frequency of the minimum modulus correlated with age in all subjects (r=0.48; P<0.0001), in men (r=0.43; P<0.005), and in women (r=0.53; P=0.001). Although several physical characteristics were associated with the frequency of the minimum modulus (bivariate correlation), a regression model that included age and these physical characteristics showed that age was the only independent predictor of the frequency of the minimum modulus. We conclude that aortic input impedance increases with advancing age in healthy men and women. This increase in aortic input impedance may be an important mechanism by which age increases the risk of cardiovascular disease in humans.
Occurrence of acrylamide carcinogen in Arabic coffee Qahwa, coffee and tea from Saudi Arabian market (2017)

The present work describes the outcomes of the assessment on acrylamide contents in a number of thermally treated foods (Arabic coffee Qahwa, coffee and tea) obtained from the Saudi Arabian markets. A total of 56 food samples of different brands and origin were studied, the amounts of acrylamide in Arabic coffee Qahwa, coffee and tea were obtained in the range of 10 to 682 μg kg<sup>-1</sup>. In comparison to coffee (152-682 μg kg<sup>-1</sup>), the Arabic coffee Qahwa (73-108 μg kg<sup>-1</sup>) and tea (10-97 μg kg<sup>-1</sup>) contain lower amounts of acrylamide. Among the analyzed samples, the green tea contained low amounts of acrylamide ranged from 10 to 18 μg kg<sup>-1</sup>, and thus the green tea could be considered as a healthier hot drink. A great variation of acrylamide formation has been observed in these food products. This divergence may be due to the initial concentration of amino acids especially asparagines and reducing sugars in food products, in addition to roasting temperature and time, pH and water activity. The obtained data can also be used in epidemiological investigation to estimate the acrylamide exposure from nutritional survey.
Calculated and observed ionization potentials of unsaturated polycyclic hydrocarbons; calculated heats of formation by several semiempirical s. c. f. m.o. methods (1970)

Abstract The ionization potentials derived from breaks in the low-resolution photoelectron spectra of several polycyclic unsaturated hydrocarbons are reported. The observed ionization potentials are compared with values calculated for semiempirical s. c .f. m. o. procedures. Calculated heats of formation for the molecules are also reported.
Regulatory CD25+ T Cells in Human Kidney Transplant Recipients (2003)

Recent evidence suggests that a population of professional regulatory cells, which limit immune responsiveness, exist in rodents and healthy human subjects. However, their role in disease states remains unclear. A proportion of renal transplant recipients do not demonstrate in vitro reactivity toward their mismatched donor-derived HLA-DR antigens; it was therefore hypothesized that this may be due to such regulatory cells. A cohort of 23 renal transplant recipients was studied at a single institution. In patients with no history of acute rejection, 6 (40%) of 15 demonstrated regulation toward the mismatched HLA-DR allopeptides by CD25(+) cells. By contrast, only one (12.5%) in eight of those with a history of acute rejection demonstrated regulation. Interestingly, if the patient assays were stratified according to initial in vitro immune responsiveness toward the mismatched allopeptides, 8 (47.1%) of 17 of patient assays with low allopeptide responsiveness (alloreactive T cell frequencies less than 60/million) demonstrated regulation of indirect pathway alloresponses by CD25(+) cells, whereas 0 of 8 with higher responses (frequencies greater than 60/million) demonstrated no such regulation (P < 0.05 by chi(2) test). The regulatory cells are present in the circulation as early as 3 mo after transplantation and persist for a number of years, despite conventional immunosuppression. Furthermore, induction treatment with anti-IL-2R mAb did not prevent the development of these regulatory CD25(+) cells. Data from two patients suggest that these cells may also play a role in preventing epitope shifting, implicated in the ongoing immune activation contributing to chronic rejection, and that loss of regulation in a given patient may precede an episode of rejection.
Responses of organic and inorganic materials to intense EUV radiation from laser-produced plasmas (2013)

We have investigated responses of polymers to EUV radiation from laser-produced plasmas beyond ablation thresholds and micromachining. We concentrated on fabricate precise 3D micro-structures of PDMS, PMMA, acrylic block copolymers (BCP), and silica. The micromachining technique can be applied to three-dimensional micro-fluidic and bio-medical devices. The EUV processing is a promising to realize a practical micromachining technique. In the present work, we used two EUV radiation sources; (a) Wide band EUV light in a range of 10{300 eV was generated by irradiation of Ta targets with Nd:YAG laser light at 500 mJ/pulse. (b) Narrow band EUV light at 11 and 13 nm was generated by irradiation of solid Xe and Sn targets, respectively, with pulsed TEA CO2 laser light. The generated EUV light was condensed onto the materials at high power density beyond the ablation thresholds, using ellipsoidal mirrors. We found that through-holes with a diameter of one micrometer an be fabricated in PMMA and PDMS sheets with thicknesses of 4-10 micrometers, at 250 and 230 nm/shot, respectively. The effective ablation of PMMA sheets can be applied to a LIGA-like process for fabricating micro-structures of metals for micro- and nano-molds. PDMS sheets are ablated if it is irradiated with EUV light beyond a distinct threshold power density, while PDMS surfaces were modified at lower power densities. Furthermore, BCP sheets were ablated to have 1-micrometer structures. Thus, we have developed a practical technique for micromachining of PMMA, PDMS and BCP sheets in a micrometer scale.
97.6% array area reduction, ReRAM computation-in-memory with hyperparameter optimization based on memory bit-error rate and bit precision of log-encoding simulated annealing (2022)

Abstract This paper proposes small array area and memory error tolerant resistive random access memory (ReRAM) computation-in-memory (CiM) with hyperparameter optimization based on bit-error rate (BER) and bit precision of log-encoding simulated annealing (SA). For combinatorial optimization problems, the proposed ReRAM CiM with log-encoding SA reduces the array area by 97.6%, compared with the conventional linear-encoding. To analyze ReRAM device error characteristics, “0” and “1” error injection is applied. The asymmetric ReRAM error improves the acceptable BER by 10 times and the acceptable bit precision to 4 bit. By adjusting the random flips and a cooling parameter, the numbers of flips and iterations decrease by 40% and 33%, respectively. Error injected (EI) iteration is changed to reproduce bit-error due to read disturb. The delay of EI iteration increases the acceptable BER by 25%. Furthermore, in the case of requiring extremely high accuracy, hyperparameter optimization improves the probability of obtaining the optimal answer by 1%.
A sweet taste receptor‐dependent mechanism of glucosensing in hypothalamic tanycytes (2017)

Hypothalamic tanycytes are glial-like glucosensitive cells that contact the cerebrospinal fluid of the third ventricle, and send processes into the hypothalamic nuclei that control food intake and body weight. The mechanism of tanycyte glucosensing remains undetermined. While tanycytes express the components associated with the glucosensing of the pancreatic β cell, they respond to nonmetabolisable glucose analogues via an ATP receptor-dependent mechanism. Here, we show that tanycytes in rodents respond to non-nutritive sweeteners known to be ligands of the sweet taste (Tas1r2/Tas1r3) receptor. The initial sweet tastant-evoked response, which requires the presence of extracellular Ca<sup>2+</sup> , leads to release of ATP and a larger propagating Ca<sup>2+</sup> response mediated by P2Y1 receptors. In Tas1r2 null mice the proportion of glucose nonresponsive tanycytes was greatly increased in these mice, but a subset of tanycytes retained an undiminished sensitivity to glucose. Our data demonstrate that the sweet taste receptor mediates glucosensing in about 60% of glucosensitive tanycytes while the remaining 40% of glucosensitive tanycytes use some other, as yet unknown mechanism.
FASTRACK (TM): Parabolic and Suborbital Experiment Support Facility (2016)

FASTRACK was developed by NASA Kennedy Space Center and Space Florida to provide capabilities to conduct frequent, affordable, and responsive flight opportunities for reduced gravity experiments, technology development, and hardware testing on suborbital vehicles and parabolic flights.
Wireless control of modular multilevel converter submodules under ac-side faults (2021)

Wireless control of modular multilevel converter (MMC) submodules has been offered recently with potentially lower cost and higher availability advantages for the converter station. In this paper, the wireless control of MMC submodules under ac-side faults is investigated. The central controller of the MMC is equipped for the unbalanced grid conditions. Local current controllers in the submodules are operated autonomously in case of loss of wireless communication during the fault. A set of simulations with single line-to-ground, line-to-line, and three-phase-to-ground faults reveal that the MMC rides through the faults in all the cases with the expected communication conditions or when the communication is lost before or after the fault instant.
Estetika přírody v estetické výchově (2012)

Magisterska diplomova prace Estetika přirody v esteticke výchově analyzuje možnosti estetiky přirody v esteticko-výchovnem procesu. Od rozebrani pojmu estetika přirody a vybraných vlivných teoretiků v tomto směru se prace zaměřuje na přitomnost, resp. nepřitomnost tohoto tematu v Ramcovem vzdělavacim programu pro gymnazia i obecne esteticke výchově. Na zakladě některých nejdůležitějsich motivů estetiky přirody, napřiklad jeji rozdilnosti od estetiky uměni, je take předkladana potencialni podoba vzdělavaciho obsahu, v němž by byla tato oblast rehabilitovana.
Analysis of clones derived from human CD7+CD4-CD8-CD3- thymocytes (1991)

The differentiation of human thymocyte precursors was studied by analysis of clonal progeny of CD4-CD8-CD3- (triple negative or TN) thymocytes. Using a culture system of phytohemagglutinin, IL-2, and irradiated allogeneic lymphoid feeder cells, we found that 48% of clones (104 total) derived from TN thymocyte suspensions were TCR gamma delta cells, 12% of clones were TCR alpha beta cells, and 34% were CD16+CD3- cells. Importantly, 6% of clones were novel subsets of CD4+CD8-CD3- or CD4-CD8+CD3- thymocytes. The majority of TCR alpha beta, TCR gamma delta, and CD16+CD3- clones expressed low levels of CD4. Molecular analysis of freshly isolated TN- thymocytes prior to in vitro culture demonstrated that up to 40% of cells had TCR gamma, delta, and beta gene rearrangements, but were negative in indirect immunofluorescence assays for cytoplasmic TCR delta and beta. These data provide evidence at the clonal level for the presence of precursors of the TCR alpha beta and TCR gamma delta lineages in the human TN thymocyte pool. Moreover, a substantial proportion of freshly isolated human TN thymocytes had already undergone TCR gene rearrangement prior to in vitro culture. Whether these precursors of the TCR alpha beta and TCR gamma delta lineages mature from cells already containing TCR gene rearrangements into sTCR+ cells or differentiate in vitro from cells with TCR genes in germline configuration remains to be determined. Nonetheless, these data demonstrate that the predominant clone types that grow out of human TN thymocytes in vitro are TCR gamma delta and NK cells.
Nanostructured biocomposite films of high toughness based on native chitin nanofibers and chitosan (2014)

Chitosan is widely used in films for packaging applications. Chitosan reinforcement by stiff particles or fibers is usually obtained at the expense of lowered ductility and toughness. Here, chitosan film reinforcement by a new type of native chitin nanofibers is reported. Films are prepared by casting from colloidal suspensions of chitin in dissolved chitosan. The nanocomposite films are chitin nanofiber networks in chitosan matrix. Characterization is carried out by dynamic light scattering, quartz crystal microbalance, field emission scanning electron microscopy, tensile tests and dynamic mechanical analysis. The polymer matrix nanocomposites were produced in volume fractions of 8, 22, and 56% chitin nanofibers. Favorable chitin-chitosan synergy for colloidal dispersion is demonstrated. Also, lowered moisture sorption is observed for the composites, probably due to the favorable chitin-chitosan interface. The highest toughness (area under stress-strain curve) was observed at 8 vol% chitin content. The toughening mechanisms and the need for well-dispersed chitin nanofibers is discussed. Finally, desired structural characteristics of ductile chitin biocomposites are discussed.
Investigation of early cancerous changes in bladder tissue by autofluorescence (2002)

Intrinsic fluorescence (autofluorescence) and reflective spectroscopy were used to study precancerous conditions and cancer in vivo in mucosal tissue of urinary bladder. Fluorescence was induced using 370 nm and 400 nm excitation, but 400 nm gave better separation of the groups. Biopsies were taken and frozen sections imaged on a fluorescence microscope with a CCD camera. The in vivo cystoscopy study had 19 patients and the cystectomy study had 35. Peak emission was 460 nm and it decreased with increased severity of disease with a 1.6 decrease from benign mucosal tissue to CIS and 3.2 decrease to invasive cancer. Invasive cancer grouped statistically differently from benign mucosal tissue using 460 nm emission while invasive cancer and CIS grouped statistically differently from benign mucosal tissue using normalized emission at 635 nm. Dysplasia did not group statistically differently from benign mucosal tissue. The fluorophores seem to be collagen and porphyrins. In microscopic images, the predominant fluorophore seems to be collagen fluorescing in blue strands while a secondary fluorophore seems to be inflammatory cells with yellowish-green round spots.
Structure-based design of AP23573, a phosphorus-containing analog of rapamycin for anti-tumor therapy. (2004)

2476 The mTOR protein, a PI3K-like kinase that links mitogenic stimuli and nutrient status to cell cycle progression, has emerged as an important target for anti-tumor therapy. Rapamycin is a natural product mTOR inhibitor that functions by inducing an inhibitory complex between the protein and cytoplasmic FKBP. The compound potently inhibits the proliferation of a wide variety of human tumor cell lines. We have used structure-based drug design to guide the synthesis of analogs of rapamycin that have optimal pharmacological properties for anti-tumor use. Computational modeling studies and previous SAR analyses indicated the possibility of replacing the C-43 secondary alcohol moiety of the cyclohexyl group of rapamycin with substituted phosphonate and phosphinate groups with retention of high-affinity binding to FKBP and mTOR. In particular, modeling indicated the existence of multiple surface residues with the potential to form favorable binding interactions with such C-43 substituents. In this study, we synthesized and evaluated a series of phosphorus-containing C43-modified rapamycin analogs. Semi-synthesis of the compounds from rapamycin using either one- or two-step conversions proceeded with high yield (>80%). Compounds were tested for FKBP binding affinity using a fluorescence polarization assay, and for the ability to inhibit the proliferation of human tumor-derived cell lines. Most of the compounds were found to have minimal reductions (less than 3-fold) in FKBP binding affinity, as predicted. In addition, the compounds inhibited the proliferation of the human fibrosarcoma cell line HT1080 with IC50 values of 0.1 –3 nM. Several of the compounds were equipotent to rapamycin in this assay (IC50 = 0.1 nM). Full details of structures and structure-activity relationships will be presented. AP23573, one of the most potent compounds, was selected for further study and development. The C43 modification of AP23573 was found to be stable in organic solvents, aqueous solutions at a variety of pHs, and in plasma and whole blood, both in vitro and in vivo. These stability studies along with in vitro metabolism studies also indicated that AP23573 is not a rapamycin pro-drug for rapamycin. AP23573 has shown potent inhibition of diverse human tumor cells lines in vitro and as xenografts implanted into nude mice. The compound is now being evaluated in phase 1 clinical trials in cancer patients.
Clock Auctions and Radio Spectrum Reallocation (2019)

We study the class of multiround, multiproduct clock procurement auctions that reduce offered prices at each round. When prices stop declining, the remaining bidders become the winning sellers. For single-minded bidders, each such auction has five properties not shared by Vickrey auctions: each is obviously strategy-proof and group-strategy-proof, sets prices that are Nash equilibrium winning bids in the related first-price auction, preserves winner privacy about values, and can be extended to satisfy a budget constraint. In simulations of the US incentive auction, a heuristic clock auction from this class achieves quick computations, high efficiency, and low prices.
A Randomized, Double-Blinded, Placebo-Controlled, Phase 2 Study of Safety, Tolerability and Efficacy of Pirfenidone in Patients with Rheumatoid Arthritis Interstitial Lung Disease (2022)

ABSTRACT Background Interstitial lung disease (ILD) is a known complication of rheumatoid arthritis (RA) with a lifetime risk in any individual of 7.7%. The TRAIL1 trial was a randomized, double-blinded, placebo-controlled, phase 2 study of safety, tolerability, and efficacy of pirfenidone for the treatment of patients with RA-ILD. Methods The TRAIL1 was a phase 2 trial intended to enroll 270 adult patients (18 to 85 years) with established RA-ILD at 33 sites in 4 countries. Patients were randomly assigned (1:1) to 2,403 mg oral pirfenidone or placebo daily. The primary endpoint was the incidence of the composite endpoint of decline from baseline in percent predicted forced vital capacity (FVC%) of 10% or greater or death during the 52-week treatment period. Key secondary endpoints included change in absolute and FVC% over 52 weeks. Findings The trial was stopped early due to slow recruitment and soon after the shutdown of clinical trials as a consequence of the coronavirus disease 2019 (COVID-19) pandemic. Data from 123 patients enrolled were analyzed. The primary endpoint was met by 11.1% on pirfenidone vs. 15% on placebo [OR=0.67 (0.22, 2.03), p=0.48]. Subjects receiving pirfenidone had a slower rate of decline in lung function as measured by estimated annual change in FVC(ml) (−66 vs. -146, p=0.0082) and FVC(%) (−1.02 vs. -3.21, p=0.0028). This effect on decline was also seen when analyzed within participants with baseline usual interstitial pneumonia (UIP) pattern on HRCT (FVC(ml) (−43 vs. -169, p=0.0014) and FVC% (−0.2 vs. -3.81, p=0.0002)). There was no significant difference in the rate of treatment-emergent serious adverse events. Interpretation Due to early termination of the study, results should be interpreted with caution. Despite being underpowered to evaluate the primary endpoint, pirfenidone slowed the rate of decline of FVC over time in subjects with RA-ILD. Safety in patients with RA-ILD was similar to that seen in other pirfenidone trials. Funding Funding for this investigator initiated trial was provided by Genentech, Inc. to Ivan O. Rosas, MD, on behalf of the TRAIL1 Investigators.
Rational Drug Design (2014)

For the past three decades rationale drug design (RDD) has been developing as an innovative, rapid and successful way to discover new drug candidates. Many strategies have been followed and several targets with diverse structures and different biological roles have been investigated. Despite the variety of computational tools available, one can broadly divide them into two major classes that can be adopted either separately or in combination. The first class involves structure-based drug design, when the target's 3-dimensional structure is available or it can be computationally generated using homology modeling. On the other hand, when only a set of active molecules is available, and the structure of the target is unknown, ligand-based drug design tools are usually used. This review describes some recent advances in rational drug design, summarizes a number of their practical applications, and discusses both the advantages and shortcomings of the various techniques used.