gebhart/patrepeval huggingface dataset:
Celebrating 5 Years of Open Access with ACS Omega (2020)

2020 marks the fifth year in which ACS Omega has published high-quality content that describes new findings in chemistry and interfacing areas of science, without any perceived evaluation of immediate impact. Since January, all front covers and much of our marketing material have included a badge commemorating this significant milestone. For us—the Editors, the journal, and the staff at ACS Publications—time seems to have passed remarkably quickly since we first set out on this mission to provide a fully open-access platform to disseminate technically sound research that advances the frontiers of science through original ideas. The journal has come a long way since the first issue in volume 1 was released in July 2016, and the quality of the work published throughout this time has been consistently high. Starting with the publication of research articles only, we then added “Perspective” and “Mini-Review” manuscript types to allow exposure of recent trends in a wide variety of areas, thus broadening the scope and appeal of the journal. The year-on-year increase in submissions and published output reflects the progress the journal has made. ACS Omega has published over 7000 articles from researchers based in 98 different countries. We received our latest impact factor of 2.87 this summer and earned 10 646 citations in 2019 (Journal Citation Reports, Clarivate), another indicator of the progress the journal has made in a short space of time. We have our Editors (both past and present), our dedicated ACS staff, our reviewers, our authors, and our readership to thank for the vital contributions they have made to the success of the journal.
The Expermental and Numerical Study of Electromigration in 2.5D Packaging (2018)

In this study, an electromigration (EM) experiment of a ball in a flip chip package with eutectic SnPb solder has been performed. The test vehicles had two types of ball grid array (BGA) interconnects between the traces: one with Cu via and one without. The package was stressed at 125oC and 150oC ambient temperature with 7A and 10A currents. Voltage and mean temperature of the test structures were measured in real-time. It was observed that the different micro-electrical structures of the two types causes great effects on the EM behavior. The time to failure (TTF) of BGA with via in the substrate is smaller than that without via. In the BGA with via, the EM-induced failure was detected at the solder ball near via, but, in BGA without via, it was found at the edge of the solder ball. A numerical simulation based on Atom Flux Divergence (AFD) was performed to understand the failure mechanism and predict the TTF. In all cases, the simulations were accurate within 10%. The accumulation of vacancies is faster in BGA with a via structure than the BGA without a via structure, and the vacancy concentration in BGA with via is almost 5 times greater than the BGA without via structure after 1000h. Thus, the BGA with via structure poses a greater chance of EM failure.
Dynamic Contact Mechanics of Radial Tears of the Lateral Meniscus: Implications for Treatment (2011)

Large RTs in the region of the popliteal hiatus show unfavorable dynamic contact mechanics.
Comparative assessment of Graves’ disease and main extrathyroidal manifestation, Graves’ ophthalmopathy, by non-targeted metabolite profiling of blood and orbital tissue (2018)

Graves' disease (GD) is an autoimmune disorder that causes the overproduction of thyroid hormones and consequent cascade of systemic metabolism dysfunction. Moreover, Graves' ophthalmopathy (GO) is the main extrathyroidal manifestation of Graves' disease (GD). The goal of the study was to identify metabolic signatures in association with diagnostic biomarkers of GD without GO and GO, respectively. Ninety metabolites were profiled and analyzed based on a non-targeted primary metabolite profiling from plasma samples of 21 GD patients without GO, 26 subjects with GO, and 32 healthy subjects. Multivariate statistics showed a clear discrimination between healthy controls and disease group (R2Y = 0.518, Q2 = 0.478) and suggested a biomarker panel consisting of 10 metabolites. Among them, most of metabolites showed the positive association with the levels of thyrotropin receptor antibodies. With combination of proline and 1,5-anhydroglucitol, which were identified as GO-specific modulators, the re-constructed biomarker model greatly improved the statistical power and also facilitated simultaneous discrimination among healthy control, GO, and GD without GO groups (AUC = 0.845-0.935). Finally, the comparative analysis of tissue metabolite profiles from GO patients proposed putative metabolic linkage between orbital adipose/connective tissues and the biofluidic consequences, in which fumarate, proline, phenylalanine, and glycerol were coordinately altered with the blood metabolites.
Tribological challenges in MEMS and their mitigation via vapor phase lubrication (2011)

MicroElectroMechanical Systems (MEMS) have become commercially successful in a number of niche applications. However, commercial success has only been possible where design, operating conditions, and materials result in devices that are not very sensitive to tribological effects. The use of MEMS in defense and national security applications will typically involve more challenging environments, with higher reliability and more complex functionality than required of commercial applications. This in turn will necessitate solutions to the challenges that have plagued MEMS since their inception - namely, adhesion, friction and wear. Adhesion during fabrication and immediately post-release has largely been resolved using hydrophobic coatings, but these coatings are not mechanically durable and do not inhibit surface degradation during extended operation. Tribological challenges in MEMS and approaches to mitigate the effects of adhesion, friction and wear are discussed. A new concept for lubrication of silicon MEMS using gas phase species is introduced. This "vapor phase lubrication" process has resulted in remarkable operating life of devices that rely on mechanical contact. VPL is also an effective lubrication approach for materials other than silicon, where traditional lubrication approaches are not feasible. The current status and remaining challenges for maturation of VPL are highlighted.
Recovery of Phosphate from Steel Manufacture Slag by Sulfuric Acid Treatment (2002)

The sulfuric acid treatment on steel manufacture slag (SMS) was performed to recover P resource. P element in SMS was successfully removed. Final products were a solid of CaSO 4 /SiO 2 and a solution containing PO 4 3 m , Fe, Al, Mg, and Mn.
Data from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk (2023)

&lt;div&gt;Abstract&lt;p&gt;Nerves are a notable feature of the tumor microenvironment in some epithelial tumors, but their role in the malignant progression of pancreatic ductal adenocarcinoma (PDAC) is uncertain. Here, we identify dense innervation in the microenvironment of precancerous pancreatic lesions, known as pancreatic intraepithelial neoplasms (PanIN), and describe a unique subpopulation of neuroendocrine PanIN cells that express the neuropeptide substance P (SP) receptor neurokinin 1-R (NK1-R). Using organoid culture, we demonstrated that sensory neurons promoted the proliferation of PanIN organoids via SP-NK1-R signaling and STAT3 activation. Nerve-responsive neuroendocrine cells exerted trophic influences and potentiated global PanIN organoid growth. Sensory denervation of a genetically engineered mouse model of PDAC led to loss of STAT3 activation, a decrease in the neoplastic neuroendocrine cell population, and impaired PanIN progression to tumor. Overall, our data provide evidence that nerves of the PanIN microenvironment promote oncogenesis, likely via direct signaling to neoplastic neuroendocrine cells capable of trophic influences. These findings identify neuroepithelial cross-talk as a potential novel target in PDAC treatment. &lt;i&gt;Cancer Res; 77(8); 1868–79. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Lessons Learned for Data-Driven Implementation Intentions with Mental Contrasting (2023)

Goal setting and realization are important but challenging. These challenges can be mitigated through effective application of behavior change realization techniques such as implementation intention and mental contrasting (IIMC). IIMC relies on identifying situations compromising desired behavior (i.e., obstacles) and creating action plans to handle those situations (i.e., identifying what, when, and where of actions to prevent or overcome the obstacles). We explore ways historical personal data can enhance the efficacy of IIMC application in the context of improving work-nonwork balance in a probing study with 16 information workers at a large technology company. We share lessons learned from this study that can help designers in further supporting goal realization with data, guide researchers interested in more formal studies of IIMC, and point the research community to important areas of future work on data-driven IIMC, particularly in the work context (e.g., the social dimensions of sense-making and planning).
Cost comparison of patients with 3-level artificial total lumbar disc replacements versus 360° fusion at 3 contiguous lumbar vertebral levels: an analysis of compassionate use at 1 site of the US investigational device exemption clinical trial (2010)

ADR-treated 3-level patients benefited from significantly lower costs from their in-hospital stay compared with those treated by fusion. Hospital service costs were 49% (54% when instrumentation was included in the costs) less for ADR patients than for fusion patients.
Gene annotation bias impedes biomedical research (2017)

1 Abstract We found tremendous inequality across gene and protein annotation resources. We observe that this bias leads biomedical researchers to focus on richly annotated genes instead of those with the strongest molecular data. We advocate for researchers to reduce these biases by pursuing data-driven hypotheses.
Tuning the magnetic properties and surface morphology of D22 Mn3-δGa films with high perpendicular magnetic anisotropy by N doping (2016)

We report the tunable magnetic properties and the smoothened surface morphology of epitaxial D022 Mn-Ga (Mn3Ga and Mn2.5Ga) films by N doping using reactive sputtering at 480 °C. The 50 nm thick Mn-Ga films grown with the N2/Ar gas flow rate (η) up to 0.66% showed 33%–50% reduction in the saturation magnetization compared to non-doped Mn-Ga. In particular, a single D022 phase was obtained in an optimal η range for Mn2.5Ga, resulted in the perpendicular magnetic anisotropy energy density of ∼1 MJ/m3 with 33% reduction in magnetization. Furthermore, the introduction of N provided the smoothened surface morphology at 50 nm thickness despite its high growth temperature, which is advantageous for thin film device applications.
Design of expert guided investigation of native L-asparaginase encapsulated long-acting cross-linker-free poly (lactic-co-glycolic) acid nanoformulation in an Ehrlich ascites tumor model (2020)

Present study explores native L-asparaginase encapsulated long-acting cross-linker-free PLGA-nanoformulation in an Ehrlich ascites tumor model. L-asparaginase-PLGA nanoparticles for tumor were prepared using a double emulsion solvent evaporation technique, optimized and validated by Box-Behnken Design. L-ASN-PNs showed a particle size of 195 nm ± 0.2 nm and a PDI of 0.2. Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) techniques revealed its smooth morphology and elicited an <i>in-vitro</i> release of 80% of the drug, following the Higuchi drug release model. <i>In-vivo</i> studies of L-ASN-PNs on an Ehrlich ascites tumor (EAT) model were completed and compared with the standard medication of 5-fluorouracil (5-FU) treatment. L-ASN-PN treated mice showed a 51.15% decrease in tumor volume and 100% survival rate with no reduction in body weight, no haemotoxicity and no hepatotoxicity, as evident from the hematological parameters, and liver enzyme parameters that were well within the prescribed limits. Chemotherapy has severe side effects and restricted therapeutic success. Henceforth, the purported L-Asparaginase PLGA nanoparticles are a suitable entity for better tumor regression, intra-tumor accumulation and no hematological side-effects.
Anion Exchange of the Cationic Layered Material [Pb2F2]2+ (2012)

We demonstrate the complete exchange of the interlamellar anions of a 2-D cationic inorganic material. The α,ω-alkanedisulfonates were exchanged for α,ω-alkanedicarboxylates, leading to two new cationic materials with the same [Pb(2)F(2)](2+) layered architecture. Both were solved by single crystal X-ray diffraction and the transformation also followed by in situ optical microscopy and ex situ powder X-ray diffraction. This report represents a rare example of metal-organic framework displaying highly efficient and complete replacement of its anionic organic linker while retaining the original extended inorganic layer. It also opens up further possibilities for introducing other anions or abatement of problematic anions such as pharmaceuticals and their metabolites.
Scale-down approach: tools for the understanding of cellulase production for 2G-bioethanol (2015)

International audience
Timing-aware control software design for automotive systems (2015)

The underlying theories of both control engineering and real-time systems engineering assume idealized system abstractions that mutually neglect central aspects of the other discipline. Control engineering theory, on the one hand, usually assumes jitter free sampling and constant input-output latencies disregarding complex real-world timing effects. Real-time engineering theory, on the other hand, uses abstract performance models that neglect the functional behavior, and derives worst-case situations that have little expressiveness for control functionalities in physically dominated automotive systems. As a consequence, there is a lot of potential for a systematic co-engineering between both disciplines, increasing design efficiency and confidence.
Inductive link design with optimal transfer efficiency and a high CMRR (2012)

In this paper, we present two key design approaches to optimize an inductive link for contactless energy transfer. Applications of the inductive link include 1.) a wireless technique to energize implanted biomedical devices; and 2.) wireless peripheral I/Os between chips. First, a new hybrid (i.e., surface mount components on a PCB) structure, which consists of a symmetrical coils and matching capacitors for improving the power link efficiency and immunity to misalignment was designed. The maximum transfer efficiency with and without impedance matching will be analyzed and shown. Since biomedical implants often relying on inductive links for power and data transfers, the interference between them is a major concern. Therefore, as the second design approach, this study proposes a full differential signaling scheme to eliminate out of band interference and provide a high CMRR in the interested frequencies. Based on EM modeling and analysis, the simulation result yields transfer responses that are in good agreement with experimental results. According to the results, the maximum transfer efficiency is 87% at 3mm vertical distance and the CMRR is higher than 50dB. At z=12mm, or a lateral misalignment of 9 mm, it is still able to achieve an optimal energy transfer (at 48%), after impedance re-matching.
Ir-catalyzed C-H functionalization of the alkaloid mitragynine – late stage selective functionalization at indole via complex core restructuring (2020)

Mitragynine, a corynanthe-type indole alkaloid, constitutes the major constituent of the plant Kratom which has a long history of use in many regions of South East Asia for treatment of various ailments including pain and opioid dependence. The use of kratom in the U.S. has been on the rise and numerous anecdotal reports suggest efficacy in self-medication for treatment-resistant
Abstract 2744: Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA (2017)

Abstract The combination of liquid biopsies and ultra-sensitive next-generation sequencing (NGS) holds tremendous promise in oncology for the detection and surveillance of somatic mutations that correlate with diagnosis, prognosis, response prediction, resistance monitoring and tumor burden. We have developed a capture-based NGS workflow that provides ultra-sensitive detection of 4 mutation classes - single nucleotide variants (SNVs), insertions/deletions, copy number amplifications (CNAs) and fusions - from low input cell-free DNA isolated from plasma. Sensitivity and specificity of 2 different AVENIO ctDNA Analysis Kits (for Research Use Only) across 3 sites for 48 samples that included contrived DNA blends with known mutations validated by digital PCR and normal reference plasma samples were assessed. The AVENIO ctDNA Targeted Kit (Targeted) was designed to detect mutations in 17 genes, across 80kb, included in NCCN Guidelines for solid tumors plus additional variants relevant for therapy selection. The AVENIO ctDNA Expanded Kit (Expanded) was designed to detect mutations in 77 genes, across 200kb, associated with solid tumor including variants relevant for clinical trial research. Testing sites achieved 100% sensitivity for SNVs and fusions at 0.5% and 1% allelic frequency, respectively, from 30 ng of input DNA for both kits. Median coverage of 4,200-6,400X was greater with the Targeted kit relative to that of 2,700-3,800X with the Expanded kit. Specificity was 100% for the Targeted kit either by sample or variant. The Expanded kit had a specificity of 91.7-100% by sample and 99.7-100% by variant. At an expected 5X or 8X copy number amplification for multiple genes, both the Targeted and Expanded kits were 100% sensitive and 93.1-98.4% specific per gene. The specificity for fusion detection was 100% for both kits down to 1% mutant allele frequency. The AVENIO ctDNA Analysis Kits for plasma and NGS applications provide exquisite sensitivity and specificity for the simultaneous detection of 4 different mutation classes. Citation Format: Stephanie Yaung, Alex Lovejoy, Dan Klass, Fergal Casey, Aruna Arcot, Melissa Loyzer, William Chiu, Nabil Azhar, Sophie Beckert, Maria Lange, Sandra Siemann, Sebastian Froehler, Shelly Gunn, John F. Palma. Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2744. doi:10.1158/1538-7445.AM2017-2744
Lanreotide for the prolonged control of carcinoid syndrome (CS) in somatostatin analog (SSA)-naïve or experienced patients. (2018)

347 Background: In the ELECT study, mean percentage of days with rescue octreotide (OCT) use was significantly lower in lanreotide depot/autogel (LAN) 120 mg vs. placebo (PBO) group during 16-week double blind (DB) phase. We examined prospective data on use of subcutaneous (sc) OCT or other medications as rescue during DB and initial open label (IOL) treatment periods of the ELECT trial to evaluate the direct impact of LAN on patients’ relief of CS symptoms for prolonged periods. Methods: Adults with neuroendocrine tumors (NETs) and CS history, with/without prior SSA use, were randomized to 16 weeks DB LAN 120 mg sc or PBO every 4 weeks, followed by a 32-week IOL LAN phase. Prospectively collected data recorded via Interactive Voice (Web) Response System on the use of sc OCT or other rescue medications during screening, DB and IOL treatment periods was analyzed. Results: During the 16-week DB phase, treatment with LAN was associated with less frequent rescue sc OCT use (least squares mean percentage of usage days (MPUD): 33.7% LAN vs. 48.5% PBO; p = 0.02). Through the 32-week LAN IOL period, rescue sc OCT use in the DB LAN group further decreased to 27.1% MPUD. Following crossover from PBO to active treatment, sc rescue OCT MPUD in the DB PBO group decreased from 48.5% to 20.9% during the IOL period. MPUD of other rescue medications at baseline were: 12.9% LAN; 8.3% PBO and no significant decreases were observed with LAN treatment during the DB phase (8.9% LAN vs. 6.3% PBO). MPUD of the DB LAN group remained relatively unchanged through the IOL phase (8.9% LAN DB; 8.8% LAN IOL). Following crossover from PBO to active treatment, the PBO group exhibited a decrease in MPUD of other rescue medications from 6.3% to 3.1% during the IOL period. Stratified by prior SSA therapy cohorts (naïve vs. prior SSA therapy), no apparent differences were observed in the use of sc OCT or other rescue medications between the two cohorts. Trends in MPUD of rescue medications of the individual cohorts were also similar to the overall group. Conclusions: The results of this study demonstrated that LAN is effective for the prolonged control of CS symptoms in SSA-naïve or experienced patients with NETs. Clinical trial information: NCT00774930.
Dynafuse (2013)

Although high-level synthesis improves FPGA productivity by enabling designers to use high-level code, the resulting performance is often significantly worse than register-transfer-level designs. One cause of such limited optimization is that high-level synthesis tools are restricted by multiple possible dependencies due to the undecidability of alias analysis. In this paper, we introduce the Dynafuse optimization, which analyzes dependencies dynamically to resolve aliases and enable runtime circuit optimizations. To resolve aliases, Dynafuse provides a specialized software data structure that dynamically determines definition-use chains between FPGA functions. In addition, Dynafuse statically creates a reconfigurable overlay network that uses detected dependencies to dynamically adjust connections between functions and memories in order to fuse pipelines and exploit data locality. Experimental results show that Dynafuse sped up two existing FPGA applications by 1.6-1.8x when exploiting locality and by 3-5x when fusing pipelines. Furthermore, the speedup from pipeline fusion increases linearly with the number of fused functions, which suggests larger applications will experience larger improvements.
Discovery of Dabrafenib: A Selective Inhibitor of Raf Kinases with Antitumor Activity against B-Raf-Driven Tumors (2013)

Hyperactive signaling of the MAP kinase pathway resulting from the constitutively active B-Raf(V600E) mutated enzyme has been observed in a number of human tumors, including melanomas. Herein we report the discovery and biological evaluation of GSK2118436, a selective inhibitor of Raf kinases with potent in vitro activity in oncogenic B-Raf-driven melanoma and colorectal carcinoma cells and robust in vivo antitumor and pharmacodynamic activity in mouse models of B-Raf(V600E) human melanoma. GSK2118436 was identified as a development candidate, and early clinical results have shown significant activity in patients with B-Raf mutant melanoma.