gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Dynamic Kinetic Resolution via Asymmetric Conjugate Reduction: Enantio‐ and Diastereoselective Synthesis of 2,4‐Dialkyl Cyclopentanones. (2002)

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.
MTADV 5-MER peptide suppresses chronic inflammations as well as autoimmune pathologies and unveils a new potential target-Serum Amyloid A (2021)

Despite the existence of potent anti-inflammatory biological drugs e.g., anti-TNF and anti IL-6 receptor antibodies, for treating chronic inflammatory and autoimmune diseases, these are costly and not specific. Cheaper oral available drugs remain an unmet need. Expression of the acute phase protein Serum Amyloid A (SAA) is dependent on release of pro-inflammatory cytokines IL-1, IL-6 and TNF-α during inflammation. Conversely, SAA induces pro-inflammatory cytokine secretion, including Th17, leading to a pathogenic vicious cycle and chronic inflammation. 5- MER peptide (5-MP) MTADV (methionine-threonine-alanine-aspartic acid-valine), also called Amilo-5MER, was originally derived from a sequence of a pro-inflammatory CD44 variant isolated from synovial fluid of a Rheumatoid Arthritis (RA) patient. This human peptide displays an efficient anti-inflammatory effects to ameliorate pathology and clinical symptoms in mouse models of RA, Inflammatory Bowel Disease (IBD) and Multiple Sclerosis (MS). Bioinformatics and qRT-PCR revealed that 5-MP, administrated to encephalomyelytic mice, up-regulates genes contributing to chronic inflammation resistance. Mass spectrometry of proteins that were pulled down from an RA synovial cell extract with biotinylated 5-MP, showed that it binds SAA. 5-MP disrupted SAA assembly, which is correlated with its pro-inflammatory activity. The peptide MTADV (but not scrambled TMVAD) significantly inhibited the release of pro-inflammatory cytokines IL-6 and IL-1β from SAA-activated human fibroblasts, THP-1 monocytes and peripheral blood mononuclear cells. 5-MP suppresses the pro-inflammatory IL-6 release from SAA-activated cells, but not from non-activated cells. 5-MP could not display therapeutic activity in rats, which are SAA deficient, but does inhibit inflammations in animal models of IBD and MS, both are SAA-dependent, as shown by others in SAA knockout mice. In conclusion, 5-MP suppresses chronic inflammation in animal models of RA, IBD and MS, which are SAA-dependent, but not in animal models, which are SAA-independent.
Growth and maturation requirements of human B cell precursors. (1992)

The present study describes our efforts to induce the proliferation of human B cell precursors (BCP). Committed BCP (CD10+, sIgM-) isolated from fetal bone marrow (18-25 weeks) were induced to proliferate at low levels in the presence of IL7. IL3 potentiated this effect of IL7 on BCP, while IL4 partially inhibited this proliferation. However, neither of these cytokines allowed the emergence of mature B cells. The growth of BCP was strongly potentiated by the presence of an adherent fibroblastic bone marrow stromal layer devoid of cells of hematopoietic origin. Addition of IL7 to such cocultures further increased BCP proliferation. BCP were shown to proliferate as stroma-adherent and non adherent cells. Total cell numbers expanded during 3 weeks, as much as 8 fold in the presence of IL7 when compared with input BCP numbers. Finally, BCP remained sIgM- in stroma dependent cultures, and only a subpopulation of cells became CD20+ in the presence of IL7. Our present study demonstrates the feasibility of human BCP expansion in vitro. However, the signals required for the transition of BCP to mature B cells remain to be determined.
(Invited, Digital Presentation) Ternary III-Sb Nanowires: Synthesis and Their Electronic and Optoelectronics Applications (2022)

Nowadays, the increasing demand for low power and highly efficient electronics and optoelectronics has driven the semiconductor industry to look for the alternatives of Si which is approaching its physical limit. Materials like graphene, carbon nanotube, III-V materials and so on, are the most promising candidates as the replacement of silicon. Among them, III-Sb materials, a sub-group of III-V materials, have been extensively researched due to their narrow and direct bandgap, high charge carrier mobility and high g-factor which makes them suitable for transistor, infra red detection and so on. Their nanowire counterparts have also been explored as the geometry of nanowire provide unique advantages. One of the research directions of III-Sb nanowire is to study their ternary counterpart (III-V-Sb or III-III’-Sb) like InAsSb, GaAsSb and InGaSb. Compares with binary compounds, ternary compound provides more room for engineering freedom like lattice parameter engineering and bandgap tuning. In this presentation, the synthesis and the electronic and optoelectronic applications of ternary III-Sb nanowires will be introduced. The high-crystal quality and high-aspect ratio ternary III-Sb nanowires were synthesized by using solid-source chemical vapor deposition method. Composition tunability was demonstrated successfully by adjusting the precursor ratio which allowed us to control the physical properties. We further integrated these nanowires into transistors and photodetectors which exhibit good performance like high carrier mobility and good photoresponse.
Site-Specific Mineralization of a Polyester Hydrolysis Product in Natural Soil (2022)

Poly(4-methylcaprolactone) (P4MCL) has been successfully incorporated into mechanically competitive materials with potential for biodegradability in engineered and natural systems. The mineralization of the hydrolysis product of P4MCL, 6-hydroxy-4-methylhexanoic acid (4MHA), was herein investigated by synthesizing tailor-made molecules with 13C labels in the carboxylic acid group (4MHA-13COOH) or the methyl group (4MHA-13CH3) and incubating each separately in a soil. Isotope-sensitive cavity ringdown spectroscopy on the efflux gas was then used to quantitatively monitor the mineralization of each isotopomer. These experiments clearly demonstrated that 4MHA was assimilated and utilized by the soil microorganisms and provided insight into position-specific mineralization. The 13CO2 evolution rate profiles and overall extents of mineralization to 13CO2 (∼85% and ∼46% for carboxyl- and methyl-labeled carbons, respectively) are consistent with the methyl carbon being preferentially incorporated into biomass rather than respired, whereas the carboxyl carbon is preferentially used for energy production and thus mineralized more rapidly (presumably by decarboxylation). These findings agree with previous reports regarding variations in the extents of mineralization of carbon atoms in different oxidation states. Moreover, this work demonstrates the value of systematically probing biodegradation of polymer hydrolysis products by the precise design of 13C-labeled molecules.
Anti-Interferon Autoantibodies in Autoimmune Polyendocrinopathy Syndrome Type 1 (2006)

These apparently spontaneous autoantibody responses to IFNs, particularly IFN-alpha and IFN-omega, segregate like a recessive trait; their high "penetrance" is especially remarkable for such a variable condition. Their apparent restriction to APS1 patients implies practical value in the clinic, e.g., in diagnosing unusual or prodromal AIRE-mutant patients with only single components of APS1, and possibly in prognosis if they prove to predict its onset. These autoantibody responses also raise numerous questions, e.g., about the rarity of other infections in APS1. Moreover, there must also be clues to autoimmunising mechanisms/cell types in the hierarchy of preferences for IFN-omega, IFN-alpha8, IFN-alpha2, and IFN-beta and IFN-lambda1.
Figure S1 from RTK-Dependent Inducible Degradation of Mutant PI3Kα Drives GDC-0077 (Inavolisib) Efficacy (2023)

&lt;p&gt;Taselisib and GDC-0077 have increased potency in PIK3CA-mutant cancer cells&lt;/p&gt;
Wafer-level technologies for computational cameras (2013)

The concept of array cameras is a new approach to imaging. It offers unique and exciting possibilities packed in very low z-height. The feature of 3-D imaging will enable new applications in smartphones and will become a must-have. Even very compact array cameras, e.g. in a 2×2 layout, deliver a high resolution video stream and a depth map without any additional hardware. On the hardware side, the lens technology is the key for computational cameras.
Outcomes of younger patients with mantle‐cell lymphoma experiencing late relapse (>24 months): the LATE‐POD study (2023)

Introduction: Patients with relapsed or refractory (R/R) mantle cell lymphoma (MCL) have poor outcome. Time to first relapse or progression (POD) has been consistently shown to be an independent predictor of survival, with patients experiencing early-POD, within 2 years since the diagnosis, representing a subgroup at greater risk of death. On the contrary, there is a paucity of large-scale treatment data on patients experiencing relapse beyond 2 years (late-POD). Methods: In this international, observational cohort study, we evaluated the outcomes amongst patients with first R/R MCL and late-POD, after upfront standard regimens including high dose cytarabine. Patients treated upfront with Bruton tyrosine kinase inhibitors (BTKi) were excluded. The primary objective was progression-free survival (PFS) of BTKi versus chemoimmunotherapy (CIT) as second line therapy. For sample size calculation 100 patients treated with drug 1 (BTKi), and 200 with drug 2 (CIT) were needed to compare PFS of drug 1 versus drug 2, assuming that CIT and BTKi would have a median PFS of 36 and 60 months, respectively. After accrual, all patients were prospectively followed-up. Overall survival (OS-2) and PFS-2 were estimated from the time of salvage therapy. Results: Overall, 386 late-POD patients were included from 10 countries. Median age was 59 (19–70), and 77% were males. Median follow-up from time of first relapse was 53 months (12–144). Overall, 114 patients had second-line BTKi (drug 1), while CIT (drug 2) was delivered to 271 patients, consisting of rituximab-bendamustine (R-B, n = 101), R-B and cytarabine (R-BAC, n = 70), or other regimens (mostly CHOP or platinum-based, n = 100). The two groups were balanced for clinicopathological features, and median time to first relapse (48 months for both). Overall, BTKi was associated with significantly longer median PFS-2 than CIT [51 versus 26 months, respectively, P = 0.0003, Figure 1], and OS-2 [88 and 56 months, P = 0.03]. The performance of BTKi and R-BAC were similar, both in terms of PFS-2 and OS-2, and significantly superior to R-B or other regimens (P = 0.0003, and P = 0.01, respectively). Multivariate Cox regression showed that ibrutinib was associated with inferior risk of death than R-B and other regimens (HR 2.41 for R-B, 2.17 for others), but similar to R-BAC. Blastoid variant, age, and time to POD as continuous variable were also independent predictors of OS-2. Nine patients with TP53 mutation had inferior OS-2 compared to TP53 wild-type patients (n = 48, P = 0.04). The research was funded by: The research was funded in part by Janssen, as part of a Clinical IIS Research Application Keywords: Aggressive B-cell non-Hodgkin lymphoma, Combination Therapies, Molecular Targeted Therapies No conflicts of interests pertinent to the abstract.
Reed-Solomon codes and multi-path strategies to improve privacy performance over ad hoc networks (2008)

This paper presents a privacy protection scheme, suitable for devices limited in CPU and/or in memory capabilities, which not only ensures anonymity and confidentiality but has also a limited impact on end-to-end network performance. Such an approach for anonymous communications, inspired by network coding techniques, benefits from recent improvements in list decoding algorithms for Reed-Solomon codes, and takes advantage of multi-path routing capabilities. The combination of these techniques is adapted for constrained and pervasive environments, such as wireless ad hoc networks, as it decreases the processing complexity of the cryptographic/decoding operations and as it ensures better tolerance to packet losses (due to mobility or to bad quality of the radio channel).
Influence of dopant ion on localized relaxation of an oxygen vacancy in stabilized zirconia (2002)

It is well known that stabilized zirconia exhibits long-range transport of oxygen ions which gives rise to diffusion relaxation of oxygen vacancies. The internal friction and the change in sound velocity in single-crystal calcia-stabilized zirconia (CSZ) doped with 12 mol % CaO were measured for longitudinal sound waves in the frequency range from 20 Hz to 700 Hz using a vibrating reed technique. In the temperature range from 300 K to 700 K, the relaxation strength exhibits strong anisotropy with respect to the directions of the k vectors. As the frequency increases the internal friction peak and the change in sound velocity shift toward high temperature, and the relaxation strength remains constant. The results show that a smaller number of oxygen vacancies contribute to diffusion relaxation than to localized relaxation, which is attributed to hopping of bound oxygen vacancies within the local structure. Comparison of the results with those reported previously for yttria-stabilized zirconia (YSZ) doped with 9.5 mol % ${\mathrm{Y}}_{2}{\mathrm{O}}_{3}$, suggests that oxygen vacancies are more strongly bound by the local structure in CSZ than in YSZ.
Optimal Load Allocation for Coded Distributed Computation in Heterogeneous Clusters (2020)

Recently, coding has been a useful technique to mitigate stragglers' effect in distributed computing. However, coding in this context has been mainly explored assuming homogeneous workers, although real-world clusters often consist of heterogeneous workers with different computing capabilities. The uniform load allocation without considering the heterogeneity possibly causes a significant loss in latency. In this article, we suggest the optimal load allocation for coded distributed computing with heterogeneous workers. Specifically, we focus on the scenario that there exist workers having the same computing capability, which can be regarded as a group for analysis. We rely on the lower bound on the expected latency and obtain the optimal load allocation by showing that our load allocation achieves the minimum of the lower bound for a sufficiently large number of workers. Given the proposed optimal load allocation, we derive the optimal code rate to achieve the minimum expected latency. From numerical simulations, when assuming the group heterogeneity, our load allocation reduces the expected latency by orders of magnitude over the existing scheme. Furthermore, from experiments on Amazon EC2 for scenarios with distinct straggler/heterogeneity patterns, we observe that our scheme outperforms the competing schemes reducing the total finishing time by up to 52%.
Runtime Prediction of Machine Learning Algorithms in Automl Systems (2023)

In this paper we introduce a metalearning-based methodology for predicting the training runtime of various machine learning algorithms. This prediction is important for automated machine learning (AutoML) systems because they search by training and evaluating a large number of machine learning models in order to identify the best model for a given dataset. Our approach identifies the main factors that impact the runtime performance of state of the art algorithms used in AutoML systems and can be used to enhance their performance in resource-constrained settings.
A Procedure for the Synthesis of Simple Spring Realizable Spatial Stiffnesses (1998)

Abstract In this paper, the synthesis of the stiffness matrices that can be realized with “simple springs” connected in parallel to a single rigid body is presented. The expression “simple spring” is used to refer to the set of elastic relations associated with passive translational springs and rotational springs. We have previously identified the realizable sub-space of stiffnesses achieved with simple springs and provided a procedure to synthesize an arbitrary full-rank stiffness matrix within this realizable subspace. In this paper, an optimization routine is used in conjunction with the synthesis procedure to obtain alternate sets of springs that better satisfy practical design considerations. The procedure presented here requires no more than 7 simple springs to realize any simple spring realizable stiffness.
Gradient nonlinearity effects on upper cervical spinal cord area measurement from 3D T1‐weighted brain MRI acquisitions (2017)

Our results raise awareness of the significant impact that GNL can have on quantitative UCCA studies, and point the way to prospectively and retrospectively managing GNL distortions in a variety of settings, including clinical environments. Magn Reson Med 79:1595-1601, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Potential involvement of DSCAML1 mutations in neurodevelopmental disorders (2021)

The molecular mechanisms underlying neurodevelopmental disorders (NDDs) remain unclear. We previously identified Down syndrome cell adhesion molecule like 1 (Dscaml1) as a responsible gene for Ihara epileptic rat (IER), a rat model for human NDDs with epilepsy. However, the relationship between NDDs and DSCAML1 in humans is still elusive. In this study, we screened databases of autism spectrum disorders (ASD), intellectual disability (ID)/developmental disorders (DD) and schizophrenia for genomic mutations in human DSCAML1. We then performed in silico analyses to estimate the potential damage to the mutated DSCAML1 proteins and chose three representative mutations (DSCAML1<sup>C729R</sup> , DSCAML1<sup>R1685*</sup> and DSCAML1<sup>K2108Nfs*37</sup> ), which lacked a cysteine residue in the seventh Ig domain, the intracellular region and the C-terminal PDZ-binding motif, respectively. In overexpression experiments in a cell line, DSCAML1<sup>C729R</sup> lost its mature N-glycosylation, whereas DSCAML1<sup>K2108Nfs*37</sup> was abnormally degraded via proteasome-dependent protein degradation. Furthermore, in primary hippocampal neurons, the ability of the wild-type DSCAML1 to regulate the number of synapses was lost with all mutant proteins. These results provide insight into understanding the roles of the domains in the DSCAML1 protein and further suggest that these mutations cause functional changes, albeit through different mechanisms, that likely affect the pathophysiology of NDDs.
Seasonal geophysical monitoring of biogenic gases in a northern peatland: Implications for temporal and spatial variability in free phase gas production rates (2008)

A set of high resolution surface ground penetrating radar (GPR) surveys, combined with elevation rod (to monitor surface deformation) and gas flux measurements, were used to investigate in situ biogenic gas dynamics within a northern peatland (Caribou Bog, Maine). Gas production rates were directly estimated from the time series of GPR measurements. Spatial variability in gas production was also investigated by comparing two sites with different geological and ecological attributes, showing differences and/or similarities depending on season. One site characterized by thick highly humified peat deposits (5–6 m), wooded heath vegetation and open pools showed large ebullition events during the summer season, with estimated emissions (based on an assumed range of CH 4 concentration) between 100 and 172 g CH 4 m −2 during a single event. The other site characterized by thinner less humified peat deposits (2–3 m) and shrub vegetation showed much smaller ebullition events during the same season (between 13 and 23 g CH 4 m −2 ). A consistent period of free‐phase gas (FPG) accumulation during the fall and winter, enhanced by the frozen surficial peat acting as a confining layer, was followed by a decrease in FPG after the snow/ice melt that released estimated fluxes between 100 and 200 g CH 4 m −2 from both sites. Estimated FPG production rates during periods of biogenic gas accumulation ranged between 0.22 and 2.00 g CH 4 m 3 d −1 and reflected strong seasonal and spatial variability associated with differences in temperature, peat soil properties, and/or depositional attributes (e.g., stratigraphy). Periods of decreased atmospheric pressure coincided with short‐period increases in biogenic gas flux, including a very rapid decrease in FPG content associated with an ebullition event that released an estimated 39 and 67 g CH 4 m −2 in less than 3.5 hours. These results provide insights into the spatial and seasonal variability in production and emission of biogenic gases from northern peatlands.
Longevity and reliability of chronic unit recordings using the Utah, intracortical multi-electrode arrays (2021)

<i>Objective.</i>Microelectrode arrays are standard tools for conducting chronic electrophysiological experiments, allowing researchers to simultaneously record from large numbers of neurons. Specifically, Utah electrode arrays (UEAs) have been utilized by scientists in many species, including rodents, rhesus macaques, marmosets, and human participants. The field of clinical human brain-computer interfaces currently relies on the UEA as a number of research groups have clearance from the United States Federal Drug Administration (FDA) for this device through the investigational device exemption pathway. Despite its widespread usage in systems neuroscience, few studies have comprehensively evaluated the reliability and signal quality of the Utah array over long periods of time in a large dataset.<i>Approach.</i>We collected and analyzed over 6000 recorded datasets from various cortical areas spanning almost nine years of experiments, totaling 17 rhesus macaques (<i>Macaca mulatta</i>) and 2 human subjects, and 55 separate microelectrode Utah arrays. The scale of this dataset allowed us to evaluate the average life of these arrays, based primarily on the signal-to-noise ratio of each electrode over time.<i>Main results.</i>Using implants in primary motor, premotor, prefrontal, and somatosensory cortices, we found that the average lifespan of available recordings from UEAs was 622 days, although we provide several examples of these UEAs lasting over 1000 days and one up to 9 years; human implants were also shown to last longer than non-human primate implants. We also found that electrode length did not affect longevity and quality, but iridium oxide metallization on the electrode tip exhibited superior yield as compared to platinum metallization.<i>Significance.</i>Understanding longevity and reliability of microelectrode array recordings allows researchers to set expectations and plan experiments accordingly and maximize the amount of high-quality data gathered. Our results suggest that one can expect chronic unit recordings to last at least two years, with the possibility for arrays to last the better part of a decade.