gebhart/patrepeval huggingface dataset:
Performance modeling for highly-threaded many-core GPUs (2014)

Highly-threaded many-core GPUs can provide high throughput for a wide range of algorithms and applications. Such machines hide memory latencies via the use of a large number of threads and large memory bandwidth. The achieved performance, therefore, depends on the parallelism exploited by the algorithm, the effectiveness of latency hiding, and the utilization of multiprocessors (occupancy). In this paper, we extend previously proposed analytical models, jointly addressing parallelism, latency-hiding, and occupancy. In particular, the model not only helps to explore and reduce the configuration space for tuning kernel execution on GPUs, but also reflects performance bottlenecks and predicts how the runtime will trend as the problem and other parameters scale. The model is validated with empirical experiments. In addition, the model points to at least one circumstance in which the occupancy decisions automatically made by the scheduler are clearly sub-optimal in terms of runtime.
Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures (2019)

We found that host-response-based diagnostics could accurately identify patients with ATB and predict individuals with high risk of progression from LTBI to ATB prior to sputum conversion. We found that a higher number of genes in a signature did not increase the accuracy of the signature. Overall, the Sweeney3 signature performed robustly across all comparisons. Our results provide strong evidence for the potential of host-response-based diagnostics in achieving the WHO goal of ending tuberculosis by 2035, and host-response-based diagnostics should be pursued for clinical implementation.
Human Factors in Medical Devices (2006)

Abstract In this article, we initially discuss human factors as defined by the FDA followed by three classic case studies. The ramifications of legal issues are then presented. Concurrent good human factors methods are then described, followed by some key topic areas including alarms, labeling, automation, and reporting. Future issues regarding human factors and medical devices are subsequently offered with conclusions and future directions of this field depicted. First, it is instructive to review the present state of affairs on how the FDA defines human factors engineering within the context of when humans interact with medical devices. The term human factors engineering is a persuasive term in the literature describing present FDA standards.
Xenon Flash Lamp‐Induced Ultrafast Multilayer Graphene Growth (2017)

Optically induced annealing technology has provided promising strategies to synthesize graphene for future flexible electronics. Focused laser‐assisted methods have the capability of direct graphene growth, but have significant drawbacks such as small beam size, and locally different intrinsic properties caused by energy variations of each pulsed shot. Herein, a novel synthesis method of multilayer graphene (MLG) via xenon flash lamp with intense and achromatic light is presented. An extremely high temperature (over 1500 °C) by a single flash irradiation induces the MLG with about 15 layers in milliseconds time scale. Experimental and theoretical studies reveal characteristics of the MLG with I 2D / I G of 0.65 and average sheet resistance of 3.272 × 10 3 Ω sq −1 as well as photothermal interactions between flash and metal catalyst. The synthesized MLG is successfully transferred onto plastic substrates, demonstrating a new feasibility of the flash lamp system for next‐generation flexible electronics.
ChemInform Abstract: ELECTRON‐TRANSFER PROCESSES: METAL SALT CATALYZED OXIDATION OF OLEFINS BY PEROXYDISULFATE (1983)

Abstract Die Reaktion von Cyclohexen (Ia) mit Peroxydisulfat unter den Bedingungen (a) (in Gegenwart von verschiedenen Metallsalzen) (b) [in Gegenwart von protonierten Basen wie (X), (XII) oder von Benzochinon (XlV)] bzw. (c) unter Bildung der angegebenen Produkte wird eingehend untersucht und mechanistisch interpretiert.
Accurate Mapping of Cleavage and Polyadenylation Sites by 3′ Region Extraction and Deep Sequencing (2014)

Deep sequencing of RNA (RNA-seq) is becoming a standard method to study gene expression. While RNA-seq reads cover most regions of an mRNA sequence, they are often depleted in the 3' end region, making them less amenable for mapping the cleavage and polyadenylation site (pA). A major problem in identification of pA is mispriming at internal A-rich regions and oligo(A) tails when an oligo(dT) primer is used for reverse transcription or sequencing. We recently developed a method named 3' region extraction and deep sequencing (3'READS), which completely addresses mispriming issues and is straightforward to use. The method accurately maps pAs and allows quantitative analysis of alternative cleavage and polyadenylation (APA) isoforms and gene expression.
Physical Aging of Polylactide-Based Graft Block Polymers (2019)

Graft block copolymers (BCPs) with poly(4-methyl caprolactone)-block-poly(±-lactide) (P4MCL-PLA) side chains containing 80–100% PLA content were synthesized with the aim of producing tough and sustainable plastics. These graft BCPs experience physical aging and become brittle over time. For short aging times, ta, the samples are ductile and shear yielding is the primary deformation mechanism. A double-yield phenomenon emerges at intermediate ta where the materials deform by stress whitening followed by shear yielding. At long ta, the samples become brittle and fail after crazing. PLA content strongly governs the time to brittle failure, where a 100% PLA graft polymer embrittles in 1 day, an 86% PLA graft BCP embrittles in 35 days, and at 80% PLA, the material remains ductile after 210 days. Molecular architecture is also a factor in increasing the persistence of ductility with time; a linear triblock ages three times faster than a graft BCP with the same PLA content. Small-angle X-ray scattering and transmission electron microscopy analysis suggest that the rubbery P4MCL domains play a role in initiating crazing by cavitation. Prestraining the graft BCPs also significantly toughens these glassy materials. Physical aging-induced embrittlement is eliminated in all of the prestrained polymers, which remain ductile after aging 60 days. The prestrained graft BCPs also demonstrate shape memory properties. When heated above the glass-transition temperature (Tg), the stretched polymer within seconds returns to its original shape and recovers the original mechanical properties of the unstrained material. These results demonstrate that graft BCPs can be used to make tough, durable, and sustainable plastics and highlight the importance of understanding the mechanical performance of sustainable plastics over extended periods of time following processing.
Comparison of the effects of class 1 and class 2 heparin‐binding growth factors on protein synthesis and actin mRNA expression in BALB/c‐3T3 cells (1988)

Biological effects of class 1 or class 2 heparin-binding growth factors (HBGFs) were compared in BALB/c-3T3 cells. Changes in protein synthesis, as monitored by two-dimensional gel electrophoresis, reveal that while both HBGFs induce the same changes in the synthesis of intracellular proteins, class 2 HBGF selectively increases the synthesis of a 43-kD extracellular protein. Heparin, which potentiates the mitogenic activity of class 1 but not class 2 HBGF, does not potentiate the changes in protein synthesis elicited by HBGF-1. Since each HBGF increases actin synthesis, regulation of actin mRNA expression was examined. Actin mRNA levels increase rapidly and transiently in response to either HBGF, and similar superinduction responses are observed in the presence of HBGF and cycloheximide. Although the maximum increase in actin mRNA stimulated by either HBGF is similar, the levels of mRNA induced by class 2 HBGF remain elevated up to 48 hours compared to the level induced by class 1 HBGF. These results imply that in the same cell type class 1 and class 2 HBGFs may modulate some biological effects differently.
Dose Escalation of Vitamin D3 Yields Similar Cryosurgical Outcome to Single Dose Exposure in a Prostate Cancer Model (2018)

Vitamin D<sub>3</sub> (VD<sub>3</sub>) is an effective adjunctive agent, enhancing the destructive effects of freezing in prostate cancer cryoablation studies. We investigated whether dose escalation of VD<sub>3</sub> over several weeks, to model the increase in physiological VD<sub>3</sub> levels if an oral supplement were prescribed, would be as or more effective than a single treatment 1 to 2 days prior to freezing. PC-3 cells in log phase growth to model aggressive, highly metabolically active prostate cancer were exposed to a gradually increasing dose of VD<sub>3</sub> to a final dose of 80 nM over a 4-week period, maintained for 2 weeks at 80 nM, and then exposed to mild sublethal freezing temperatures. Results demonstrate that both acute 24-hour exposure to 80 nM VD<sub>3</sub> and dose escalation resulted in enhanced cell death following freezing at -15°C or colder, with no significant differences between the 2 exposure regimes. Apoptotic analysis within the initial 24-hour period postfreeze revealed that VD<sub>3</sub> treatment induced both caspase 8- and 9-mediated cell death, most notably in caspase 8 at 8-hour postfreeze. These results indicate that both the intrinsic and extrinsic apoptotic pathways are involved in VD<sub>3</sub> sensitization prior to freezing. Additionally, both acute and gradual dose escalation regimes of VD<sub>3</sub> exposure increase prostate cancer cell sensitivity to mild freezing. Importantly, this study expands upon previous reports and suggests that the combination of VD<sub>3</sub> and freezing may offer an effective treatment for both slow growth and highly aggressive prostate cancers.
Concurrent and parallel transmissions are optimal for low data-rate IR-UWB networks (2008)

The Internet of Things, emerging pervasive and sensor networks are low data-rate wireless networks with, a priori, no specific topology and no fixed infrastructure. Their primary requirements are twofold: first, low power consumption and, due to environmental concerns, low emitted power. Second, robustness to poor propagation environments and multi-user interference. Impulse-radio ultra-wide band (IR-UWB) physical layers have the potential to satisfy these requirements. Because the features of IR-UWB physical layers differ from narrow-band physical layers, the design rules of IR-UWB networks are likely to be different than for narrow-band wireless networks. Indeed, to optimally use the resources available, it is crucial for the network layers to take into account and take advantage of the underlying physical layer. Therefore, we are interested in the design of IR-UWB networks in a low data-rate, self-organized, and multi-hop context. We concentrate on the medium access control (MAC) layer and the physical layer. In the case of low data-rate IR-UWB networks, the optimal design is to allow for parallel and concurrent transmissions at the MAC layer. Interference is managed with rate adaptation, no power control and an interference mitigation scheme at the physical layer. A protocol that implements the optimal design and allows for parallel transmissions outperforms protocols that use exclusion or power control.
The neuraminidase of bat influenza viruses is not a neuraminidase (2012)

Influenza A viruses are classified into subtypes according to their two viral glycoproteins, hemagglutinin (HA) and neuraminidase (NA). These viruses are known to infect multiple animal species, including humans, pigs, horses, dogs, sea mammals, chickens, ducks, and other birds. Although humans are sporadically infected with avian influenza virus strains belonging to multiple subtypes, only H1, H2, and H3 HA subtypes and N1 and N2 NA subtypes have been documented to cause pandemics and annual epidemics of influenza in humans. By contrast, all H16 and N9 subtypes of influenza A viruses are found circulating in birds. The recent discovery of influenza A viruses clearly distinct from any known avian influenza A virus subtype in little yellow-shouldered bats from Guatemala has been the first example of an influenza A virus subtype not found in avian species (1). Bat influenza viruses have glycoproteins related to the HA and NA of influenza A virus, which prompted to the classification of these viruses as H17N10 influenza A virus. The crystal structure of the N10 glycoprotein is now solved independently by Li et al. (2) and Zhu et al. (3) in PNAS, and these works provide important clues on the characteristics of these newly discovered influenza viruses.
Antifungal activity of selected Malassezia indolic compounds detected in culture (2019)

Malassezia yeasts produce indolic species that inhibit an array of clinically significant yeasts and moulds.
Cover Image, Volume 123, Number 3, March 1, 2021 (2021)

The cover image is based on the Review Article The Evolving Landscape of Immunotherapy in Solid Tumors by Michael Lowe et al., https://doi.org/10.1002/jso.26416.
Formation and Decomposition of Water Soluble Colloidal Manganese Dioxide During the Reduction of by Cysteine. A Kinetic Study (2008)

Upon addition of cysteine to a solution of , a transient species appears within the time of mixing, which is stable for several months. In order to conform the nature of the transient species, spectroscopic, kinetic and coagulation experiments were carried out. For the formation of water-soluble colloidal MnO2, the stiochiometry was found to be 1:1 (cysteine:). On adding of HClO4, there is a decrease in the absorbance of colloidal MnO2. At higher [cysteine] (≥2.0 × 10−4 mol dm−3), as the reaction became so fast, the formation and decomposition of colloidal MnO2 are not observed. Thus in presence of [HClO4] and excess of [cysteine], the intermediate colloidal MnO2 is unstable. Kinetic studies of the decomposition of water soluble colloidal MnO2 have been investigated by visible spectrophotometry at 25°C. The observed kinetics was explained by assuming fast adsorption of cysteine on the surfaces of colloidal MnO2. The adsorption formation constants between MnO2-cysteine and MnO2-F− have been determined (Kad = 8.5 × 103 dm3 mol−1 and Kf = 4.9 × 104 dm3 mol−1 for cysteine and F−, respectively). The deposition of solid MnO2 was observed in presence of externally added Mn(II) and Ag+ ions. On the basis of the various observations, a most plausible mechanism has been envisaged for the decomposition of water soluble colloidal MnO2.
Synchronization of intonation adjustments in violin duets: towards an objective evaluation of musical interaction (2011)

In ensemble music performance, such as a string quartet or du et, the musicians interact and influence each other’s performance via a multitude of parameters – including tempo, dynamics, articulation of musical phrases and, depending on the type of instrument, intonation. This paper presents our ongoing research on the effect of interaction between violinists, in terms of intonation. We base our analysis on a series of experiments with professional as well as amateur musicians playing in duet and solo experimental set-ups, and then apply a series of interdependence measures on each violinist’s pitch deviations from the score. Our results show that while it is possible to, solely based on intonation, distinguish between solo and duet performances for simple cases, there is a multitude of underlying factors that need to be analyzed before these techniques can be applied to more complex pieces and/or non-experimental situations.
Synthesis of organophosphates starting from α-hydroxyphosphonates (2018)

α-Hydroxyphosphonates were successfully converted to the corresponding phosphates applying the phospha-Brook rearrangement under phase transfer catalytic conditions. Among several possible catalysts tested, K2CO3, Cs2CO3, as well as modified Moroccan phosphates were found to be suitable.
Predicting Energy Measurements of Service-Enabled Devices in the Future Smartgrid (2010)

In the future Internet of Things devices will generate massive amounts of data that will flow to enterprise systems and provide a timely view on the execution of business processes. Being able to estimate data generated by devices may have significant effects on planning and execution of business applications. We present some methodologies for mining data gathered from devices in the energy domain i.e. web service enabled smart meters and home appliances. We present here an approach that realise short-term prediction based on neural networks or support vector machines. We consider detailed information about energy consumption coming from service-enabled devices in the broader smart grid envisioned future infrastructure.
Laser pixelation of thick scintillators for medical imaging applications: x-ray studies (2013)

To achieve high spatial resolution required in nuclear imaging, scintillation light spread has to be controlled. This has been traditionally achieved by introducing structures in the bulk of scintillation materials; typically by mechanical pixelation of scintillators and fill the resultant inter-pixel gaps by reflecting materials. Mechanical pixelation however, is accompanied by various cost and complexity issues especially for hard, brittle and hygroscopic materials. For example LSO and LYSO, hard and brittle scintillators of interest to medical imaging community, are known to crack under thermal and mechanical stress; the material yield drops quickly with large arrays with high aspect ratio pixels and therefore the pixelation process cost increases. We are utilizing a novel technique named Laser Induced Optical Barriers (LIOB) for pixelation of scintillators that overcomes the issues associated with mechanical pixelation. In this technique, we can introduce optical barriers within the bulk of scintillator crystals to form pixelated arrays with small pixel size and large thickness. We applied LIOB to LYSO using a high-frequency solid-state laser. Arrays with different crystal thickness (5 to 20 mm thick), and pixel size (0.8×0.8 to 1.5×1.5 mm<sup>2</sup>) were fabricated and tested. The width of the optical barriers were controlled by fine-tuning key parameters such as lens focal spot size and laser energy density. Here we report on LIOB process, its optimization, and the optical crosstalk measurements using X-rays. There are many applications that can potentially benefit from LIOB including but not limited to clinical/pre-clinical PET and SPECT systems, and photon counting CT detectors.
Investigation of the magnetic structures in giant magnetoresistive multilayer films by electron microscopy (1994)

The magnetic structures which occur in (Co/Ni81Fe19/Co)/Cu multilayer films showing giant magnetoresistance have been investigated using electron microscopy. Rather similar fine domains, with sub-μm dimensions, were found in films comprising 14 and 6 magnetic layers. Whilst the observed structure depended greatly on the magnetic history of the sample, a combination of differential phase contrast imaging and low angle diffraction allowed an estimate to be made of the extent to which neighboring magnetic layers were aligned antiparallel to each other. For both samples typically two layers were found to have parallel alignment leading to the possibility that departures from the expected antiferromagnetic behavior are more prevalent at the surfaces rather than in the bulk of the multilayer.
15-PGDH inhibition activates the splenic niche to promote hematopoietic regeneration (2021)

The splenic microenvironment regulates hematopoietic stem and progenitor cell (HSPC) function, particularly during demand-adapted hematopoiesis; however, practical strategies to enhance splenic support of transplanted HSPCs have proved elusive. We have previously demonstrated that inhibiting 15-hydroxyprostaglandin dehydrogenase (15-PGDH), using the small molecule (+)SW033291 (PGDHi), increases BM prostaglandin E2 (PGE2) levels, expands HSPC numbers, and accelerates hematologic reconstitution after BM transplantation (BMT) in mice. Here we demonstrate that the splenic microenvironment, specifically 15-PGDH high-expressing macrophages, megakaryocytes (MKs), and mast cells (MCs), regulates steady-state hematopoiesis and potentiates recovery after BMT. Notably, PGDHi-induced neutrophil, platelet, and HSPC recovery were highly attenuated in splenectomized mice. PGDHi induced nonpathologic splenic extramedullary hematopoiesis at steady state, and pretransplant PGDHi enhanced the homing of transplanted cells to the spleen. 15-PGDH enzymatic activity localized specifically to macrophages, MK lineage cells, and MCs, identifying these cell types as likely coordinating the impact of PGDHi on splenic HSPCs. These findings suggest that 15-PGDH expression marks HSC niche cell types that regulate hematopoietic regeneration. Therefore, PGDHi provides a well-tolerated strategy to therapeutically target multiple HSC niches, promote hematopoietic regeneration, and improve clinical outcomes of BMT.
Enhanced Analysis and Design Method of Concurrent Dual-Band Power Amplifiers With Intermodulation Impedance Tuning (2013)

The behavior of power amplifiers (PAs) driven by concurrent dual-band signals is analyzed theoretically in this paper. According to the analysis, the impedance matching at intermodulation (IM) frequency is very important for PAs working in concurrent mode. Based on the concept of IM impedance tuning, a family of new operation modes can be introduced, including concurrent Class-A, Class-AB, Class-B, and Class-C. The theoretical performance of these modes are derived and the overdrive effects of them are also discussed. A possible structure is proposed to implement the proposed IM impedance tuning, and a concurrent Class-AB dual-band example PA operating at 1.9-2.6-GHz long-term evolution (LTE) bands is demonstrated. Experimental results show good consistence with the theoretical analysis, and the concurrent Class-AB PA prototype exhibits higher than 36.1% power-added efficiency in concurrent mode when driven by 10- and 15-MHz LTE signals in two bands concurrently. To our best knowledge, this is the state-of-the-art efficiency performance of concurrent dual-band PAs, even higher than previously reported dual-band Doherty PAs. Additionally the proposed PA, which is fabricated using a 10-W GaN HEMT, can output more than 34.3-dBm power with a peak-to-average ratio of 7 dB in concurrent mode, showing a remarkable power utilization factor for concurrent dual-band PAs.
Short Vi-polysaccharide abrogates T-independent immune response and hyporesponsiveness elicited by long Vi-CRM197conjugate vaccine (2020)

Polysaccharide-protein conjugates have been developed to overcome the T-independent response, hyporesponsiveness to repeated vaccination, and poor immunogenicity in infants of polysaccharides. To address the impact of polysaccharide length, typhoid conjugates made with short- and long-chain fractions of Vi polysaccharide with average sizes of 9.5, 22.8, 42.7, 82.0, and 165 kDa were compared. Long-chain-conjugated Vi (165 kDa) induced a response in both wild-type and T cell-deficient mice, suggesting that it maintains a T-independent response. In marked contrast, short-chain Vi (9.5 to 42.7 kDa) conjugates induced a response in wild-type mice but not in T cell-deficient mice, suggesting that the response is dependent on T cell help. Mechanistically, this was explained in neonatal mice, in which long-chain, but not short-chain, Vi conjugate induced late apoptosis of Vi-specific B cells in spleen and early depletion of Vi-specific B cells in bone marrow, resulting in hyporesponsiveness and lack of long-term persistence of Vi-specific IgG in serum and IgG<sup>+</sup> antibody-secreting cells in bone marrow. We conclude that while conjugation of long-chain Vi generates T-dependent antigens, the conjugates also retain T-independent properties, leading to detrimental effects on immune responses. The data reported here may explain some inconsistencies observed in clinical trials and help guide the design of effective conjugate vaccines.