gebhart/patrepeval huggingface dataset:
FIGHT: A randomized, double-blind, placebo-controlled, phase II study of bemarituzumab (bema) combined with modified FOLFOX6 in 1L FGFR2b+ advanced gastric/gastroesophageal junction adenocarcinoma (GC). (2021)

4010 Background: Bema is a first-in-class humanized IgG1 monoclonal antibody selective for fibroblast growth factor receptor 2b (FGFR2b). Results from the FIGHT study showed an improvement in progression-free survival (PFS), overall survival (OS), and overall response rate with the addition of bema to mFOLFOX6 in FGFR2b+, non HER2+ GC. This report provides updated analyses of patient (pt) subgroups, additional data on ocular adverse events (AEs), and the median OS result for the bema+mFOLFOX6 combination. Methods: Pts were treated with mFOLFOX6 and randomized 1:1 to bema (15 mg/kg) or placebo (pbo) every 2 weeks (wks) with an additional 7.5 mg/kg bema/pbo dose on cycle 1 day 8. Eligible pts had unresectable locally advanced or metastatic GC not known to be HER2+, and had FGFR2b overexpression (any 2+/3+ staining) by centrally performed immunohistochemistry (IHC+) or FGFR2 amplification by circulating tumor DNA (ctDNA+). Results: Of the 155 pts who were randomized, 149 (96%) were FGFR2b+ by IHC, 26 (17%) by ctDNA, and 20 (13%) by both. 96 pts (62%) had tumors with FGFR2b IHC 2+/3+ in ≥10% of tumor cells. The proportion of pts with ctDNA+ or with ≥5% or ≥10% tumor cells FGFR2b+ by IHC was similar across geographic regions. Bema showed a benefit vs pbo across pre-specified subgroups including age, gender, geographic region, and prior adjuvant therapy. Patients with FGFR2b overexpression irrespective of ctDNA gene amplification benefited from bema: IHC+/ctDNA- PFS hazard ratio (HR) 0.63 (95% CI 0.4, 0.99), OS HR 0.66 (95% CI 0.39, 1.12); IHC+/ctDNA+ PFS HR 0.15 (95% CI 0.02, 1.18), OS HR 0.10 (95% CI 0.01, 0.83). Frequency and severity of ocular AEs were similar for the overall enrolled population and for pts with ≥5% or ≥10% FGFR2b+ by IHC. Corneal AEs in the bema arm increased in frequency and severity over time; 10.5% (0% G3) wk 1-8 vs 44.1% (15.3% G3) wk ≥25. Following discontinuation of study treatment, subsequent anti-cancer therapy was balanced in the 2 arms (bema 53%; pbo 49%). With a median follow-up of 12.5 months (mo), the bema arm had a median OS of 19.2 mo (95%CI: 13.6, not reached) vs 13.5 mo (95%CI: 9.3, 15.9) for placebo (HR:0.60 95%CI: 0.38, 0.94) for the intent-to-treat population; for the subset of pts with ≥10% FGFR2b+ by IHC, the median OS for bema was 25.4 mo (95%CI: 13.8, not reached) vs 11.1 mo (95% CI: 8.4, 13.8) for placebo (HR: 0.41 95%CI: 0.23, 0.74). Conclusions: The addition of bema to mFOLFOX6 improved the OS of 1L FGFR2b+ GC pts vs mFOLFOX6 alone. Outcomes favored bema across pre-specified subgroups. Pts with overexpression of FGFR2b even without ctDNA amplification demonstrated a benefit from the addition of bema to mFOLFOX6, supporting further evaluation of bema in tumors with FGFR2b overexpression without the requirement for gene amplification. Clinical trial information: NCT03694522.
Figure S3 from NRF2 Activation Promotes Aggressive Lung Cancer and Associates with Poor Clinical Outcomes (2023)

&lt;p&gt;Fig. S3, related to Fig. 3.&lt;/p&gt;
Image quality assessment to enhance infrared face recognition (2017)

Automatic quality evaluation of infrared images has not been researched as extensively as for images of the visible spectrum. Moreover, there is a lack of studies on the influence of degradation of image quality on the performance of computer vision tasks operating on thermal images. Here, we quantify the impact of common image distortions on infrared face recognition, and present a method for aggregating perceptual quality-aware features to improve the identification rates. We use Natural Scene Statistics (NSS) to detect degradation of infrared images, and to adapt the face recognition algorithm to the quality of the test image. The proposed approach applied to a face identification algorithm based on thermal signatures yielded an improvement of rank one recognition rates between 11% and 19%. These results confirm the relevance of image quality assessment for improving biometric identification systems that use thermal images.
Complexity in microseismic phase identification: full waveform modelling, traveltime computations and implications for event locations within the Groningen gas field (2019)

Determining accurate microseismic event locations at the Groningen gas field in the Netherlands has important implications for understanding the ongoing induced seismicity and its associated seismic hazard. To improve the depth constraint of the microseismicity, downhole monitoring arrays have been deployed in the central region of the Groningen field. The observed seismicity at these receivers is characterized by significant complexity in the waveforms, due to the high velocity contrasts that exist and the acquisition geometry. Reliably identifying and picking phases for use in earthquake location algorithms is therefore particularly challenging. Using a well constrained and highly detailed 3-D velocity model, we show how full waveform modelling can be used to understand the causes of the observed phase complexity. By identifying the different modelled phase arrivals in detail, we look to identify any systematic changes in waveform complexity with source location, to aid phase identification of the recorded downhole data. Theoretical traveltimes are often the foundation of earthquake location algorithms. We highlight the associated problems of their computation for the downhole monitoring setup for the Groningen model by complementing the full waveform simulations with traveltime computations and their associated ray paths from both an eikonal solver and using the wavefront construction method. We highlight large inconsistencies in the traveltimes, demonstrate the limitations and sensitivity of ray tracing in a layered velocity model, and show how the theoretical traveltimes do not equate with the dominant phase arrivals observed within the modelled waveforms. Finally, we propose an approach based on computing P- and S-wave traveltimes directly from the full waveform modelling, such that phase picking is based on an amplitude threshold rather than individual phase identification, which can also be adjusted for any given moment tensor.
Neuroimaging mechanisms of acupuncture on functional reorganization for post-stroke motor improvement: a machine learning-based functional magnetic resonance imaging study (2023)

https://www.chictr.org.cn/showproj.html?proj=37359, ChiCTR1900022220.
Copper‐Catalyzed Carbonylative Hydroamidation of Styrenes to Branched Amides (2020)

Abstract Amides are one of the most ubiquitous functional groups in synthetic and medicinal chemistry. Novel and rapid synthesis of amides remains in high demand. In this communication, a general and efficient procedure for branch‐selective hydroamidation of vinylarenes with hydroxyamine derivatives enabled by copper catalysis has been developed for the first time. The reaction proceeds under mild conditions and tolerates a broad range of functional groups. Applying a chiral phosphine ligand, an enantioselective variant of this transformation was achieved, affording a variety of chiral α‐amides with excellent enantioselectivities (up to 99 % ee ) and high yields.
A multimodal learning interface for sketch, speak and point creation of a schedule chart (2004)

We present a video demonstration of an agent-based test bed application for ongoing research into multi-user, multimodal, computer-assisted meetings. The system tracks a two person scheduling meeting: one person standing at a touch sensitive whiteboard creating a Gantt chart, while another person looks on in view of a calibrated stereo camera. The stereo camera performs real-time, untethered, vision-based tracking of the onlooker's head, torso and limb movements, which in turn are routed to a 3D-gesture recognition agent. Using speech, 3D deictic gesture and 2D object de-referencing the system is able to track the onlooker's suggestion to move a specific milestone. The system also has a speech recognition agent capable of recognizing out-of-vocabulary (OOV) words as phonetic sequences. Thus when a user at the whiteboard speaks an OOV label name for a chart constituent while also writing it, the OOV speech is combined with letter sequences hypothesized by the handwriting recognizer to yield an orthography, pronunciation and semantics for the new label. These are then learned dynamically by the system and become immediately available for future recognition.
Microscopy of Polyurea Grease (2020)

Understanding the physical structure of greases can provide critical insight into improving the lubricating performance of a grease. Observation of the grease structure can be quite difficult depending on the type of grease and the length scale of the structure. Polyurea greases in previous reports have typically been examined by removal of the oil phase, which significantly changes the polyurea structure. This paper examines the effect of sample preparation conditions on the microstructure of polyurea greases. This study reveals new structures in the polyurea that have not been observed in the previous literature, including entangled fibers and nanotubes. Correlation is found between the observed polyurea microstructure coverage and grease stiffness.
Identification of H. volcanii Phosphomevalonate Decarboxylase and Isopentenyl Phosphate Kinase as Catalysts of the Terminal Enzymatic Reactions in an Archaeal Alternate Mevalonate Pathway (LB139) (2014)

To identify the enzymes responsible for metabolism of mevalonate 5‐phosphate to isopentenyl diphosphate in H. volcanii, two open reading frames (HVO_2762; HVO_1412) were selected for expression and characterization. Characterization of these proteins indicates that one enzyme is an isopentenyl phosphate kinase that forms isopentenyl diphosphate. The second enzyme exhibits a decarboxylase activity that has never been directly attributed to this protein or any homologous protein. It catalyzes the synthesis of isopentenyl phosphate from mevalonate 5‐phosphate, a reaction proposed but never demonstrated by direct experimental proof. This enzyme, phosphomevalonate decarboxylase (PMD), exhibits strong inhibition by 6‐fluoromevalonate monophosphate but negligible inhibition by 6‐fluoromevalonate diphosphate (a potent inhibitor of the classical mevalonate pathway), reinforcing its selectivity for monophosphorylated ligands. Inhibition by the fluorinated analog also suggests that the PMD utilizes a reaction mechanism similar to that demonstrated for the classical MVA pathway decarboxylase. These observations represent the first experimental demonstration in H. volcanii of both the phosphomevalonate decarboxylase and isopentenyl phosphate kinase reactions that are required for an alternate mevalonate pathway in an archaeon. These results also represent, to the best of our knowledge, the first identification and characterization of an archaeal phosphomevalonate decarboxylase.
Continuous-Flow Graph Transportation Distances (2016)

Optimal transportation distances are valuable for comparing and analyzing probability distributions, but larger-scale computational techniques for the theoretically favorable quadratic case are limited to smooth domains or regularized approximations. Motivated by fluid flow-based transportation on $\mathbb{R}^n$, however, this paper introduces an alternative definition of optimal transportation between distributions over graph vertices. This new distance still satisfies the triangle inequality but has better scaling and a connection to continuous theories of transportation. It is constructed by adapting a Riemannian structure over probability distributions to the graph case, providing transportation distances as shortest-paths in probability space. After defining and analyzing theoretical properties of our new distance, we provide a time discretization as well as experiments verifying its effectiveness.
Feature replacement methods enable reliable home video analysis for machine learning detection of autism (2020)

Autism Spectrum Disorder is a neuropsychiatric condition affecting 53 million children worldwide and for which early diagnosis is critical to the outcome of behavior therapies. Machine learning applied to features manually extracted from readily accessible videos (e.g., from smartphones) has the potential to scale this diagnostic process. However, nearly unavoidable variability in video quality can lead to missing features that degrade algorithm performance. To manage this uncertainty, we evaluated the impact of missing values and feature imputation methods on two previously published autism detection classifiers, trained on standard-of-care instrument scoresheets and tested on ratings of 140 children videos from YouTube. We compare the baseline method of listwise deletion to classic univariate and multivariate techniques. We also introduce a feature replacement method that, based on a score, selects a feature from an expanded dataset to fill-in the missing value. The replacement feature selected can be identical for all records (general) or automatically adjusted to the record considered (dynamic). Our results show that general and dynamic feature replacement methods achieve a higher performance than classic univariate and multivariate methods, supporting the hypothesis that algorithmic management can maintain the fidelity of video-based diagnostics in the face of missing values and variable video quality.
Ultralight Conductive Silver Nanowire Aerogels (2017)

Low-density metal foams have many potential applications in electronics, energy storage, catalytic supports, fuel cells, sensors, and medical devices. Here, we report a new method for fabricating ultralight, conductive silver aerogel monoliths with predictable densities using silver nanowires. Silver nanowire building blocks were prepared by polyol synthesis and purified by selective precipitation. Silver aerogels were produced by freeze-casting nanowire aqueous suspensions followed by thermal sintering to weld the nanowire junctions. As-prepared silver aerogels have unique anisotropic microporous structures, with density precisely controlled by the nanowire concentration, down to 4.8 mg/cm<sup>3</sup> and an electrical conductivity up to 51 000 S/m. Mechanical studies show that silver nanowire aerogels exhibit "elastic stiffening" behavior with a Young's modulus up to 16 800 Pa.
Platelet Function and Plasma Fibrinogen and their Relations to Gender, Smoking Habits, Obesity and Beta-Blocker Treatment in Young Survivors of Myocardial Infarction (1988)

Seventy-three (58 men and 15 women) survivors of myocardial infarction below 45 years of age and 73 healthy matched controls were investigated regarding in vitro platelet aggregability to ADP and collagen, platelet sensitivity to prostacyclin and plasma levels of beta-thromboglobulin, platelet factor 4 and fibrinogen. The patients, studied 3-6 months after the acute event, had a reduced platelet sensitivity to prostacyclin. They did not differ from the controls regarding the other platelet function tests. Females had higher platelet reactivity than men. Smoking, obesity or beta-blocker treatment did not influence platelet function. The patients had higher fibrinogen levels than the controls. Gender did not influence, while smoking and obesity increased plasma fibrinogen. Patients on beta-blockade had lower fibrinogen levels than patients without this therapy. The high fibrinogen level and the low platelet sensitivity to prostacyclin might indicate an increased thrombotic liability in young myocardial infarction patients.
Strain Sensors: A Highly Aligned Nanowire‐Based Strain Sensor for Ultrasensitive Monitoring of Subtle Human Motion (Small 24/2020) (2020)

In article number 2001363, Weiwei Wu, Hossam Haick, and co-workers develop a highly sensitive strain sensor based on nanowires. The nanowires prepared by a capillarity-inspired imprinting method have an aligned pattern, ensuring the reproducibility of strain sensor fabrication. The nanowire-based strain sensor exhibits versatile and superior sensing performance for subtle human motion monitoring.
Martensitic Transformation and Shape Memory Effect in Ausaged Fe-Ni-Si Alloys. (2002)

Martensitic transformations in the Fe–(24–30)Ni–(5–8)Si(mass%) alloys have been investigated by means of optical and transmission electron microscopy, differential scanning calorimetry and hardness-testing. The Ms temperature is decreased by Si addition and the morphology of martensite is mainly lenticular in the unaged specimens. However, a pronounced decrease in the Ms temperature and a change in the martensite morphology from the lenticular to the thin plate type are observed on ausaging at 400°C. The increase in austenite hardness, the decrease in the Ms temperature and the increase in the tetragonality of martensite after ausaging at 400°C are clarified as due to the formation of nanoscale particles of γ'-(Ni, Fe)3Si with the L12 structure during ausaging at 400°C. The Fe–Ni–Si alloys that form thin plate martensite show the shape memory effect, which arises from the reverse transformation of stress-induced martensite to austenite. Precipitation hardening of the austenite phase by fine γ' particles during ausaging improves the degree of shape recovery.
Superior growth performance in broiler chicks fed chelated compared to inorganic zinc in presence of elevated dietary copper (2016)

Dietary 250 mg/kg Cu significantly impaired feed intake and weight gain in birds fed ZnSO4 · H2O, but had less impact in birds fed Zn(HMTBa)2. No difference was observed between the two organic zinc sources. These results are consistent with the hypothesis that chelated organic Zn is better utilized than inorganic zinc in the presence of elevated Cu.
The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus (2005)

Telomerase replicates chromosome ends, a function necessary for maintaining genome integrity. We have identified the gene that encodes the catalytic reverse transcriptase (RT) component of this enzyme in the malaria parasite Plasmodium falciparum (PfTERT) as well as the orthologous genes from two rodent and one simian malaria species. PfTERT is predicted to encode a basic protein that contains the major sequence motifs previously identified in known telomerase RTs (TERTs). At approximately 2500 amino acids, PfTERT is three times larger than other characterized TERTs. We observed remarkable sequence diversity between TERT proteins of different Plasmodial species, with conserved domains alternating with hypervariable regions. Immunofluorescence analysis revealed that PfTERT is expressed in asexual blood stage parasites that have begun DNA synthesis. Surprisingly, rather than at telomere clusters, PfTERT typically localizes into a discrete nuclear compartment. We further demonstrate that this compartment is associated with the nucleolus, hereby defined for the first time in P.falciparum.
Vulnerability of the superficial zone of immature articular cartilage to compressive injury (2010)

Objective The zonal composition and functioning of adult articular cartilage causes depth-dependent responses to compressive injury. In immature cartilage, shear and compressive moduli as well as collagen and sulfated glycosaminoglycan (sGAG) content also vary with depth. However, there is little understanding of the depth-dependent damage caused by injury. Since injury to immature knee joints most often causes articular cartilage lesions, this study was undertaken to characterize the zonal dependence of biomechanical, biochemical, and matrix-associated changes caused by compressive injury. Methods Disks from the superficial and deeper zones of bovine calves were biomechanically characterized. Injury to the disks was achieved by applying a final strain of 50% compression at 100%/second, followed by biomechanical recharacterization. Tissue compaction upon injury as well as sGAG density, sGAG loss, and biosynthesis were measured. Collagen fiber orientation and matrix damage were assessed using histology, diffraction-enhanced x-ray imaging, and texture analysis. Results Injured superficial zone disks showed surface disruption, tissue compaction by 20.3 ± 4.3% (mean ± SEM), and immediate biomechanical impairment that was revealed by a mean ± SEM decrease in dynamic stiffness to 7.1 ± 3.3% of the value before injury and equilibrium moduli that were below the level of detection. Tissue areas that appeared intact on histology showed clear textural alterations. Injured deeper zone disks showed collagen crimping but remained undamaged and biomechanically intact. Superficial zone disks did not lose sGAG immediately after injury, but lost 17.8 ± 1.4% of sGAG after 48 hours; deeper zone disks lost only 2.8 ± 0.3% of sGAG content. Biomechanical impairment was associated primarily with structural damage. Conclusion The soft superficial zone of immature cartilage is vulnerable to compressive injury, causing superficial matrix disruption, extensive compaction, and textural alteration, which results in immediate loss of biomechanical function. In conjunction with delayed superficial sGAG loss, these changes may predispose the articular surface to further softening and tissue damage, thus increasing the risk of development of secondary osteoarthritis.
Acceleration of Frequent Itemset Mining on FPGA using SDAccel and Vivado HLS (2017)

Frequent itemset mining (FIM) is a widely-used data-mining technique for discovering sets of frequently-occurring items in large databases. However, FIM is highly time-consuming when datasets grow in size. FPGAs have shown great promise for accelerating computationally-intensive algorithms, but they are hard to use with traditional HDL-based design methods. The recent introduction of Xilinx SDAccel development environment for the C/C++/OpenCL languages allows developers to utilize FPGA's potential without long development periods and extensive hardware knowledge. This paper presents an optimized implementation of an FIM algorithm on FPGA using SDAccel and Vivado HLS. Performance and power consumption are measured with various datasets. When compared to state-of-the-art solutions, this implementation offers up to 3.2× speedup over a 6-core CPU, and has a better energy efficiency as compared with a GPU. Our preliminary results on the new XCKU115 FPGA are even more promising: they demonstrate a comparable performance with a state-of-the-art HDL FPGA implementation and better performance compared to the GPU.