gebhart/patrepeval huggingface dataset:
Fluororescence in situ hybridization (FISH) gene amplification analysis of EGFR and HER2 in patients with malignant salivary gland tumors (MSGT) treated with lapatinib (2007)

C41 Background. MSGT are a heterogeneous group of malignancies with distinct histologies and variable biological behavior. In a previously reported phase II trial of the dual EGFR/HER2 tyrosine kinase inhibitor lapatinib in progressive MSGT, prolonged disease stabilization of > 6 months was observed in 36% of evaluable patients (pts) [Agulnik et al, J Clin Oncol 2007]. MSGT pts were divided into 2 cohorts in this trial: adenoid cystic carcinoma (ACC) and non-adenoid cystic carcinoma (non-ACC).  Methods. FISH analysis for both EGFR and HER2 gene amplification was performed successfully in the archival tumor specimens of 20 pts with ACC and 17 pts with non-ACC, all treated with lapatinib. For EGFR, high polysomy and gene amplification would qualify as being FISH positive. For HER2, specimens were determined to be amplified if the ratio of HER2 signals to chromosome 17 centromere (CEP17) signals was > 2.0.  Results. For ACC, no EGFR or HER2 gene amplifications were detected. For non-ACC, no EGFR gene amplifications were detected but 3 pts (18%) were HER2 amplified. All 3 HER2 amplified non-ACC pts had poorly differentiated histologies (1 squamous, 2 adenocarcinomas), and all had stained 3+ for both EGFR and HER2 by immunohistochemistry in their archival specimens. Only 2 of these 3 pts were evaluable for efficacy as 1 pt never received lapatinib, and these 2 pts have time-to-progression (TTP) duration of 8.3 months (mo) and 18.4 mo. For pts with both FISH and efficacy outcome data, the HER2 to CEP17 ratio was explored to determine its predictive value for TTP. Interestingly, when this ratio was stratified as low ( 1.1), pts with low and high ratios had a prolonged TTP than those with moderate ratios. For ACC pts, the TTP of pts with low/high ratios was 9.5 mo versus 3.1 mo for those with moderate ratios (p = 0.03). For non-ACC pts, the TTP of pts with low/high ratios was 8.3 mo versus 1.6 mo for those with moderate ratios (p = 0.015).  Conclusions. EGFR gene amplifications were not found in MSGT. HER2 gene amplifications using conventional criteria were not found in ACC, but were found in a minority of non-ACC MSGT pts, all of whom had 3+ HER2 staining by immunohistochemistry. Pts with low or high HER2 to CEP17 FISH ratios appear to have a longer TTP than those with moderate ratios, perhaps reflecting improved clinical outcomes in a dual pt population. A low HER2 to CEP17 FISH ratio may have prognostic value and reflects pts who have a less aggressive disease biology, whereas a high HER2 to CEP17 FISH ratio may have predictive value and reflects pts who benefited most from lapatinib. Further exploration of this as a marker of efficacy is warranted.
Swapping of the β-Hairpin Region between Sp1 and GLI Zinc Fingers:  Significant Role of the β-Hairpin Region in DNA Binding Properties of C<sub>2</sub>H<sub>2</sub>-type Zinc Finger Peptides (2005)

The recent design strategy of zinc finger peptides has mainly focused on the alpha-helix region, which plays a direct role in DNA recognition. On the other hand, the study of non-DNA-contacting regions is extremely scarce. By swapping the beta-hairpin regions between the Sp1 and GLI zinc fingers, in this study, we investigated how the beta-hairpin region of the C(2)H(2)-type zinc finger peptides contributes to the DNA binding properties. Surprisingly, the Sp1 mutant with the GLI-type beta-hairpin had a higher DNA binding affinity than that of the wild-type Sp1. The result of the DNase I footprinting analyses also showed the change in the DNA binding pattern. In contrast, the GLI zinc finger completely lost DNA binding ability as a result of exchanging the beta-hairpin region. These results strongly indicate that the beta-hairpin region appears to function as a scaffold and has an important effect on the DNA binding properties of the C(2)H(2)-type zinc finger peptides.
Directing lateral growth of lithium dendrites in micro-compartmented anode arrays for safe lithium metal batteries (2018)

Uncontrolled growth of lithium dendrites during cycling has remained a challenging issue for lithium metal batteries. Thus far, various approaches have been proposed to delay or suppress dendrite growth, yet little attention has been paid to the solutions that can make batteries keep working when lithium dendrites are already extensively present. Here we develop an industry-adoptable technology to laterally direct the growth of lithium dendrites, where all dendrites are retained inside the compartmented copper current collector in a given limited cycling capacity. This featured electrode layout renders superior cycling stability (e.g., smoothly running for over 150 cycles at 0.5 mA cm<sup>-2</sup>). Numerical simulations indicate that reduced dendritic stress and damage to the separator are achieved when the battery is abusively running over the ceiling capacity to generate protrusions. This study may contribute to a deeper comprehension of metal dendrites and provide a significant step towards ultimate safe batteries.
<sup>13</sup>C and <sup>139</sup>La NMR Studies of La<sub>2</sub>@C<sub>80</sub>: First Evidence for Circular Motion of Metal Atoms in Endohedral Dimetallofullerenes (1997)

Clear confirmation of recent theoretical studies concerning the structure of the endohedral complexes formed by La and C80 is provided by the NMR spectroscopic investigations presented here Complex La2@C80 is present, and its structure is based on the unstable “empty” Ih isomer of C80. The two La atoms circulate inside this round cage even at room temperature (shown schematically on the right).
Histamine Dihydrochloride For the Treatment of Acute Myeloid Leukemia, Malignant Melanoma and Renal Cell Carcinoma (2008)

Histamine dihydrochloride is a vasoactive biogenic amine. It inhibits the reactive oxygen species formation in monocytes via histamine H2 receptors and protects natural killer and T cells from oxidative damage. Histamine has the potential to optimize cytokine-induced activation of T cells and natural killer cells; therefore, the addition of histamine to cytokine treatment may improve treatment efficacy. Clinical trials in solid tumors and in acute myeloid leukemia have demonstrated the potential to improve treatment outcome when histamine dihydrochloride is combined with immunotherapy. In patients with metastatic malignant melanoma, this strategy improved remission rates and increased survival. On the other hand, less promising results were reported for histamine dihydrochloride added to cytokines in patients with other solid tumors, especially in advanced renal cell carcinoma. A recent international Phase III trial performed in 320 patients showed that maintenance therapy with histamine dihydrochloride and IL-2 was able to improve leukemia-free survival in patients with acute myeloid leukemia, without an effect on overall survival. The combination of histamine dihydrochloride with IL-2 potentially offers an efficacious and tolerable maintenance strategy for patients with acute myeloid leukemia; however, its impact on survival remains to be explored.
Subunit Vaccines Against Emerging Pathogenic Human Coronaviruses (2020)

Seven coronaviruses (CoVs) have been isolated from humans so far. Among them, three emerging pathogenic CoVs, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and a newly identified CoV (2019-nCoV), once caused or continue to cause severe infections in humans, posing significant threats to global public health. SARS-CoV infection in humans (with about 10% case fatality rate) was first reported from China in 2002, while MERS-CoV infection in humans (with about 34.4% case fatality rate) was first reported from Saudi Arabia in June 2012. 2019-nCoV was first reported from China in December 2019, and is currently infecting more than 70000 people (with about 2.7% case fatality rate). Both SARS-CoV and MERS-CoV are zoonotic viruses, using bats as their natural reservoirs, and then transmitting through intermediate hosts, leading to human infections. Nevertheless, the intermediate host for 2019-nCoV is still under investigation and the vaccines against this new CoV have not been available. Although a variety of vaccines have been developed against infections of SARS-CoV and MERS-CoV, none of them has been approved for use in humans. In this review, we have described the structure and function of key proteins of emerging human CoVs, overviewed the current vaccine types to be developed against SARS-CoV and MERS-CoV, and summarized recent advances in subunit vaccines against these two pathogenic human CoVs. These subunit vaccines are introduced on the basis of full-length spike (S) protein, receptor-binding domain (RBD), non-RBD S protein fragments, and non-S structural proteins, and the potential factors affecting these subunit vaccines are also illustrated. Overall, this review will be helpful for rapid design and development of vaccines against the new 2019-nCoV and any future CoVs with pandemic potential. This review was written for the topic of <i>Antivirals for Emerging Viruses: Vaccines and Therapeutics</i> in the <i>Virology</i> section of <i>Frontiers in Microbiology</i>.
Design, Performance Prediction, and Validation of a Seed Orienting Corn Planter (2013)

<abstract> <bold>Abstract.</bold> Investigations into active control of corn canopy architecture through manipulation of seed orientation at planting have shown that specific seed orientations produce highly aligned leaf azimuths. Data obtained from hand planted field trials with across-row oriented leaves show that such canopies intercept more light and ultimately produce higher yields. This study was conducted to investigate the feasibility of mechanized seed orientation through the concept of part orientation by pushing. 3D-scans of 15 âmedium flatâ kernels of the hybrids DKC-6342, DKC-6346, P0902HR and P1162HR have been computationally analyzed to determine stable seed orientations when subjected to pushing. These predicted results were compared to data obtained in bench tests. The concept was then refined and integrated into a prototype planter based on a standard off-the-shelf row unit. The prototype was tested in a soil bin at laboratory conditions. The computational model was able to predict seed orientation by pushing very accurately. The analysis and subsequent bench unit and prototype tests revealed that orientation performance is dependent on seed shape with the kernels of DKC-6342 being the most and those of P1162HR the least suitable. Soil bin experiments confirmed that at least parity between seed and ground velocity must be achieved in order to maintain orientation during transition from the orientation mechanism to the ground.
A multi-threshold wavelet coder (MTWC) for high fidelity image compression (2002)

An embedded wavelet coder algorithm which adopts different threshold values in different subbands is proposed in this work. The new image coder, called the multi-threshold wavelet coder (MTWC), achieves a better rate-distortion performance than existing embedded wavelet coders for applications requiring higher quality with higher bit rates (e.g. greater than 1 bpp). Another advantage of MTWC is its lower computational complexity. The superior performance of MWC can be explained by examining the evolution of the distortion distribution in each subband as image data are compressed in the embedded coding process. Experimental results are given to demonstrate the performance of MTWC at various bit rates.
Contour Detection of the Left Ventricular Cavity from Angiographic Images (1985)

A knowledge-based heuristic method is proposed to outline the left ventricular cavity from end-diastolic angiographic images in right anterior oblique projection in man. The algorithm search for the optimal path in a weighted graph, representing the state space, can implicitly be defined as the set of all the contour segments that can be produced by successor operators. Applications to routine images are presented.
Finger-Wheel Cultivators for High-Speed Cultivation of Vegetable Crops (2008)

ABSTRACT The Precision Cultural System (PCS) developed by the Louisiana Agricultural Experiment Station allows simple and precise cultivation of vegetable crops; however, speed of the cultivators in small vegetable crops has been limited. The standard PCS sweep cultivator was limited to about 1–1f mph in small crops because it would throw soil over the crop plants at higher speed. The standard PCS rotary tiller cultivator could operate at 2–3 mph in small crops but could not be operated faster in larger crops, due to its tendency to “walk out of the soil at higher speeds”. The standard PCS sweep cultivator was modified by replacing the sweeps between the twin drills with two pairs of straight finger-wheel (rolling cultivator) spiders non-angled and in tandem. The finger-wheel gangs on the bed sides were also inactivated by raising them above the soil. The resulting PCS cultivator was successfully operated in very small crop plants (≤ 1 inch high) at speeds of 5–6 mph with no crop damage. The cultivato...
A psychological approach to understanding the social and language impairments in autism (1999)

This paper surveys current research on the social and communicative impairments in autism. In diagnostic schemes, the criteria for identifying autism in these domains include overlapping features. One approach to interpreting this overlap is to consider that social and communicative impairments reflect the same underlying cognitive deficit, referred to as the 'theory of mind' hypothesis of autism. On this view autism involves primary difficulties in identifying mental states in other people, and in interpreting behavior and action in relation to a person's mental state. Studies on the relationship between social behavior, communicative functioning, and theory of mind in children with autism are reviewed, emphasizing the connections between these areas of impairment that are central to the definition of the autistic syndrome.
Copper metabolism in mottled mouse mutants. The effect of copper therapy on lysyl oxidase activity in brindled (<i>Mobr</i>) mice (1982)

Lysyl oxidase activity in extracts of skin from 1-day-old Mobr/Y mice was found to be between 50 and 60% of that in corresponding extracts from littermate +/Y mice of the same age. It was increased to 84-150% of that in the latter by prior treatment of the Mobr/Y mice at 7 days of age with a single subcutaneous injection of 50 micrograms of copper, retained as Cu+ in an alkyl polyether/sebacic acid solution. This suggests that in this form the copper is able to by-pass the block in copper metabolism and is deliverable to copper-requiring processes.
Insulin-Like Growth Factor-1 Inscribes a Gene Expression Profile for Angiogenic Factors and Cancer Progression in Breast Epithelial Cells (2002)

Activation of the insulin-like growth factor-1 receptor (IGF-1R) by IGF-1 is associated with the risk and progression of many types of cancer, although despite this it remains unclear how activated IGF-1R contributes to cancer progression. In this study, gene expression changes elicited by IGF-1 were profiled in breast epithelial cells. We noted that many genes are functionally linked to cancer progression and angiogenesis. To validate some of the changes observed, the RNA and/or protein was confirmed for c-fos, cytochrome P450 1A1, cytochrome P450 1B1, interleukin-1 beta, fas ligand, vascular endothelial growth factor, and urokinase plasminogen activator. Nuclear proteins were also temporally monitored to address how gene expression changes were regulated. We found that IGF-1 stimulated the nuclear translocation of phosphorylated AKT, hypoxic-inducible factor-1 alpha, and phosphorylated cAMP-responsive element-binding protein, which correlated with temporal changes in gene expression. Next, the promoter regions of IGF-1-regulated genes were searched in silico. The promoters of genes that clustered together had similar regulatory regions. In summary, IGF-1 inscribes a gene expression profile relevant to cancer progression, and this study provides insight into the mechanism(s) whereby some of these changes occur.
mRNA quality control: An ancient machinery recognizes and degrades mRNAs with nonsense codons (2007)

Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway which ensures the rapid degradation of mRNAs containing premature translation termination codons (PTCs or nonsense codons), thereby preventing the accumulation of truncated and potentially harmful proteins. In this way, the NMD pathway contributes to suppressing or exacerbating the clinical manifestations of specific human genetic disorders. Studies in model organisms have led to the identification of the effectors of the NMD pathway, and illuminated the mechanisms by which premature stops are discriminated from natural stops, so that only the former trigger rapid mRNA degradation. These studies are providing important insights that will aid the development of new treatments for at least some human genetic diseases.
Al-Coated Conductive Fiber Filters for High-Efficiency Electrostatic Filtration: Effects of Electrical and Fiber Structural Properties (2018)

Through the direct decomposition of an Al precursor ink AlH<sub>3</sub>{O(C<sub>4</sub>H<sub>9</sub>)<sub>2</sub>}, we fabricated an Al-coated conductive fiber filter for the efficient electrostatic removal of airborne particles (>99%) with a low pressure drop (~several Pascals). The effects of the electrical and structural properties of the filters were investigated in terms of collection efficiency, pressure drop, and particle deposition behavior. The collection efficiency did not show a significant correlation with the extent of electrical conductivity, as the filter is electrostatically charged by the metallic Al layers forming electrical networks throughout the fibers. Most of the charged particles were collected via surface filtration by Coulombic interactions; consequently, the filter thickness had little effect on the collection efficiency. Based on simulations of various fiber structures, we found that surface filtration can transition to depth filtration depending on the extent of interfiber distance. Therefore, the effects of structural characteristics on collection efficiency varied depending on the degree of the fiber packing density. This study will offer valuable information pertaining to the development of a conductive metal/polymer composite air filter for an energy-efficient and high-performance electrostatic filtration system.
Toward a synergy between p2p and grids (2003)

Peer-to-peer (P2P) networks and grids are distributed computing models that enable decentralized collaboration by integrating computers into networks in which each can consume and offer services. P2P is a class of self-organizing systems or applications that takes advantage of distributed resources storage, processing, information, and human presence available at the Internet's edges. A grid is a geographically distributed computation platform comprising a set of heterogeneous machines that users can access through a single interface. Both are hot research topics because they offer promising paradigms for developing efficient distributed systems and applications. Unlike the classic client-server model, in which roles are well separated, P2P and grid networks can assign each node a client or server role according to the operations they are to perform on the network - even if some nodes act more as server than as client in current implementations. In spite of current practices and thoughts, the grid and P2P models share several features and have more in common than we perhaps generally recognize. It is time to consider how to integrate these two models. A synergy between the two research communities, and the two computing models, could start with identifying the similarities and differences between them.
Reductive Dehalogenations of Halobenzoates by Anaerobic Lake Sediment Microorganisms (1983)

Methane-producing freshwater lake sediment was found to dehalogenate chloro-, bromo-, and iodobenzoates by a reductive reaction in which the halogen was replaced by a hydrogen atom. The identity of the dehalogenated products was confirmed by mass spectrometry, nuclear magnetic resonance, or cochromatography. Removal of the halogens to produce benzoate was necessary before mineralization to CH(4) + CO(2) could occur. The dehalogenation occurred after a lag period which lasted from 1 week to more than 6 months, depending on the chemical. Dehalogenation was not observed in the absence of CH(4) production, and it was inhibited by the addition of 20% O(2). Once sediment was acclimated to halobenzoate dehalogenation, new additions of the halobenzoate were degraded without lag. Acclimation was observed regardless of whether the parent substrates were eventually mineralized to CH(4) + CO(2). Sediment acclimated to bromo- and chlorobenzoate degradation generally metabolized bromo- and chlorobenzoates, but sediment acclimated to iodobenzoate degradation only metabolized iodobenzoate. Prior acclimation of sediment to benzoate decomposition did not alter the pattern of dehalogenation, and sediment acclimated to dehalogenation was not concurrently acclimated to benzoate degradation. The presence of this apparent specificity, the lag period, and subsequent acclimation, together with our findings of the absence of dehalogenation in sterile sediments and by sediments previously incubated at >/=39 degrees C, suggests that this reaction was biologically catalyzed. Apparently, a pathway for the reductive dehalogenation of aryl halides is present in anaerobic microorganisms of this methanogenic sediment.
Mononuclear Cell Factor--Interleukin-1 in Rheumatoid Arthritis (1985)

Connective (issue destruction including bone rcsorption arc salient pathological features of chronic inflammatory diseases such as rheumatoid arthritis. These processes arc in part related to the high level of collagenasc and PGE, present within the synovium and the synovial fluid Initial studies indicate that the fibroblastic cells cultured from rheumatoid synovium are the principal sources of collagenasc and PGE,. It is reasonable to assume that these cells arc derived from proliferation of cells present in the synovium prior to the initiation of inflammation. The mononuclcarccll factor (MCF) produced by monocytcs and macrophages from the blood, synovial fluid and pannus stimulates the production of collagenasc and PGE, by fibroblastoid synovial cells. MCF shares chemical and biological properties with IL-1. MCF/IL-1 appears to play a pivotal role in communication between immune and non-immunc cells during chronic inflammation, since lymphocytes and lymphocyte products lead to an increased production of MCF/IL-1 in the presence of antigen. MCF/IL-1 modulates the morphology, replication and responsiveness of synovial cells to hormones, as well as stimulating these cells to produce collagenasc and PGE, In addition. MCF/IL-1 is involved in the reparativc processes which also occur in rheumatoid arthritis