gebhart/patrepeval huggingface dataset:
Automated Multiplex Immunofluorescence Panel for Immuno-oncology Studies on Formalin-fixed Carcinoma Tissue Specimens (2019)

Continued developments in immuno-oncology require an increased understanding of the mechanisms of cancer immunology. The immunoprofiling analysis of tissue samples from formalin-fixed, paraffin-embedded (FFPE) biopsies has become a key tool for understanding the complexity of tumor immunology and discovering novel predictive biomarkers for cancer immunotherapy. Immunoprofiling analysis of tissues requires the evaluation of combined markers, including inflammatory cell subpopulations and immune checkpoints, in the tumor microenvironment. The advent of novel multiplex immunohistochemical methods allows for a more efficient multiparametric analysis of single tissue sections than does standard monoplex immunohistochemistry (IHC). One commercially available multiplex immunofluorescence (IF) method is based on tyramide-signal amplification and, combined with multispectral microscopic analysis, allows for a better signal separation of diverse markers in tissue. This methodology is compatible with the use of unconjugated primary antibodies that have been optimized for standard IHC on FFPE tissue samples. Herein we describe in detail an automated protocol that allows multiplex IF labeling of carcinoma tissue samples with a six-marker multiplex antibody panel comprising PD-L1, PD-1, CD68, CD8, Ki-67, and AE1/AE3 cytokeratins with 4′,6-diamidino-2-phenylindole as a nuclear cell counterstain. The multiplex panel protocol is optimized in an automated IHC stainer for a staining time that is shorter than that of the manual protocol and can be directly applied and adapted by any laboratory investigator for immuno-oncology studies on human FFPE tissue samples. Also described are several controls and tools, including a drop-control method for fine quality control of a new multiplex IF panel, that are useful for the optimization and validation of the technique.
Engineering as a Space of White Privilege (2015)

Engineering has had a continual concern with diversity due to the low numbers of minority and female majors. Although race is recognized as socially constructed, the rhetoric around race in engineering for the most part takes it as an immutable characteristic of certain individuals (Black, Hispanic, Native American, etc.). Further, the approach to improving diversity takes on a Colonial perspective, with programs to help these students better “assimilate” into college life and to “fix” their perceived deficiencies in basic math and science. Some authors have examined the experiences of various minorities within engineering. However, there is almost no work that examines the privileges that inherently accrue to the majority white male in engineering. I take a Critical White perspective and build on Peggy McIntosh’s concept of the “invisible knapsack” to describe how I, as a white, heterosexual, Protestant, male, was inherently advantaged throughout my career as an engineer.
Y-Junction-Coupled S-Section InAs/InGaAs/GaAs Quantum-Dot Ring Lasers with High Unidirectionality (2007)

Fabrication and characterization of Y-junction-coupled S-section InAs/InGaAs/GaAs quantum dot ring lasers with high unidirectionality is reported. The new design suppresses the unwanted counterpropagating modes more effectively than in the previous S-section-racetrack design.
Significant Effect of Carbonate Ions on the Photooxidation of Water on Mesoporous TiO2 Film Electrodes (2002)

Abstract Carbonate ions cause a net increase of the saturation photocurrent as well as the occurrence of a stepwise photocurrent/potential (I/V) characteristic for the photooxidation of water at a nanocrystalline TiO2 photoanode deposited on the conducting glass.
Design of a superconducting linac cavity for high current energy recovery linac operation (2004)

The RHIC electron cooler as well as other applications (such as a linac-ring version of eRHIC) requires a very high average current CW electron linac in an energy recovery mode. In this paper we present the design of a 5-cell superconducting linac cavity for velocity of light particles. This cavity will operate at 703.75 MHz with a large beam pipe aperture of 19 cm diameter and ferrite HOM absorbers in the beam pipe, in addition to the conventional HOM couplers for low frequency HOMs. We will report the design of the cavity geometry using the BuildCavity and Superfish codes, loss factor simulations with ABCI, detailed HOM simulations with MAFIA (with and without the ferrite absorbers) and beam breakup simulations using the code TDBBU.
Dominant Expression of the CysLT<sub>2</sub>Receptor Accounts for Calcium Signaling by Cysteinyl Leukotrienes in Human Umbilical Vein Endothelial Cells (2003)

HUVECs almost exclusively express the CysLT2R. Furthermore, Ca2+ fluxes elicited by CysLT in these cells emanate from perturbation of the CysLT2R, rather than the expected CysLT1R. Hence, signaling events involving CysLT2R might trigger functional responses involved in the critical components of LT-dependent vascular reactions, which in turn have implications for ischemic heart disease and myocardial infarction.
An Analysis of Size USA Men`s Body Shapes for Developing Menswear Sizing Systems (2011)

The menswear industry is an important segment of the U.S. apparel business. Sales in the menswear market have been steadily growing over the past decade, especially in the luxury business (Business Wire, 2007; Kolesnikov-Jessop, 2010; Reuters, 2010). While the rate of growth slowed dramatically in late 2008 and 2009, due to a global economic downturn, the market is still of major importance to the industry. Retailers, designers, and leading luxury brands (such as Roberto Cavalli, Georgio Armani, etc) are being more cautious about what they offer, aiming to provide value to the consumer and to pay closer attention to men’s needs (Reuters, 2010) which are constantly evolving. Size indicators relate to dimensions of a garment component relative to a particular body dimension such as collar or inseam. The production of tailored men's clothing is a complicated process and is hindered by the dimensional sizing system currently in use (Stone, 2007). There have been a number of attempts during the last decade to gather anthropometric data that would allow a better understanding of the adult population. In the United Sates, the SizeUSA national sizing survey was led by [TC]2, a nonprofit organization. A representative sample of the entire male and female U.S. population was recorded by scanning over 10,000 people in 13 cities ([TC], 2004). To date however, there has been no in-depth analysis comparing men's body shape and menswear sizing systems that might reveal factors that underlie fit problems. Therefore, the purpose of this study was to specifically evaluate the relationship of the drop to men's body shapes, and in general to determine if there are any easily identifiable changes in men’s body shapes that should be taken into account in the current sizing standards.
Biologically-inspired locomotion of a 2g hexapod robot (2010)

Here we present the design, modeling, and fabrication of a 2g mobile robot. By applying principles from biology and existing meso-scale fabrication techniques, a 5.7cm hexapod robot with sprawled posture has been created, and is capable of locomotion up to 4 body-lengths per second using the alternating tripod gait at 20Hz actuation frequency. Furthermore, this work proves the viability of a new mechanical linkage design, fabricated using the smart composite microstructure process, to provide desirable leg trajectories for successful ambulation at the insect-scale.
The paraphrase search assistant (1999)

We present a new linguistic approach to the construction of terminological feedback for use in interactive query refinement. The method exploits the tendency for key domain concepts within result sets to participate in families of semantically related lexical compounds. We outline an algorithm for computing a ranked list of result set "themes" and describe a web application, the Paraphrase Search Assistant, designed to make use of the theme extraction algorithm to support a recognition-based, iterative information seeking dialog.
Atomically thin layers of MoS<sub>2</sub>via a two step thermal evaporation–exfoliation method (2011)

Two dimensional molybdenum disulfide (MoS(2)) has recently become of interest to semiconductor and optic industries. However, the current methods for its synthesis require harsh environments that are not compatible with standard fabrication processes. We report on a facile synthesis method of layered MoS(2) using a thermal evaporation technique, which requires modest conditions. In this process, a mixture of MoS(2) and molybdenum dioxide (MoO(2)) is produced by evaporating sulfur powder and molybdenum trioxide (MoO(3)) nano-particles simultaneously. Further annealing in a sulfur-rich environment transforms majority of the excess MoO(2) into layered MoS(2). The deposited MoS(2) is then mechanically exfoliated into minimum resolvable atomically thin layers, which are characterized using micro-Raman spectroscopy and atomic force microscopy. Furthermore Raman spectroscopy is employed to determine the effect of electrochemical lithium ion exposure on atomically thin layers of MoS(2).
ChemInform Abstract: A Simple, General and Stereoselective Synthesis of 1‐(Dialkoxyboryl)‐1, 3‐dienes (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Structural Optimization of Enantiopure 2‐Cyclialkylamino‐2‐aryl‐1,1‐diphenylethanols as Catalytic Ligands for Enantioselective Additions to Aldehydes. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 2 from Local HPV Recombinant Vaccinia Boost Following Priming with an HPV DNA Vaccine Enhances Local HPV-Specific CD8&lt;sup&gt;+&lt;/sup&gt; T-cell–Mediated Tumor Control in the Genital Tract (2023)

&lt;p&gt;Characterization of MAdCAM-1 expression in cervicovaginal tissue after vaccination&lt;/p&gt;
Supramolecular Polymeric Materials with Hierarchical Structure-Within-Structure Morphologies (1999)

Hierarchical structure-within-structure morphologies are reported here as being directly imaged for the first time using transmission electron microscopy (TEM). These images reveal that the two structures are oriented perpendicular to the block-copolymer intermaterial dividing surface. The Figure shows a hexagonal array of polystyrene cylinders embedded in a lamellar matrix.
Export Performance and Competitiveness of the Irish Economy (2005)

This paper reviews Ireland’s recent export performance, with emphasis on the reasons behind the strong gains in market share experienced by the economy over the past 15 years.
Geometric decorrelation in acoustic tools for surveying the seafloor (2012)

International audience
Interaction of Adipokines and Hepatitis B Virus on Histological Liver Injury in the Chinese (2009)

TNF-alpha and/or IL-6 contribute to hepatic necroinflammation in chronic hepatitis B patients. Adiponectin protects against insulin resistance and hepatic steatosis but does not affect liver injury. Adipokines and viral factors contribute to liver injury independently.
From text to prosody without toBI (2002)

A new method for predicting prosodic parameters, i.e. phone durations and F0 targets, from preprocessed text is presented.The prosody model comprises a set of CARTs, which are learned from a large database of labeled speech.This database need not be annotated with Tone and Break Indices (ToBI labels).Instead, a simpler symbolic prosodic description is created by a bootstrapping method.The method had been applied to one Spanish and two German speakers.For the German voices, two listening tests showed a significant preference for the new method over a more traditional approach of prosody prediction, based on hand-crafted rules.
Tandem duplications of 7q34 and 3q25 in pilocytic astrocytoma result in RAF fusion genes (2010)

Pilocytic astrocytoma (PA) is the most common childhood brain tumor (WHO I) and typically shows no malignant progression. Molecular mechanisms of PA formation remained poorly defined until recently, when we idenfidied tandem duplications at 7q34 as a hallmark genetic lesion in PA. These duplicationsresult in BRAF fusion genes and lead to constitutive MAPK activation.
Dynamic Steerable Blocks in Deep Residual Networks (2017)

Filters in convolutional networks are typically parameterized in a pixel basis, that does not take prior knowledge about the visual world into account. We investigate the generalized notion of frames designed with image properties in mind, as alternatives to this parametrization. We show that frame-based ResNets and Densenets can improve performance on Cifar-10+ consistently, while having additional pleasant properties like steerability. By exploiting these transformation properties explicitly, we arrive at dynamic steerable blocks. They are an extension of residual blocks, that are able to seamlessly transform filters under pre-defined transformations, conditioned on the input at training and inference time. Dynamic steerable blocks learn the degree of invariance from data and locally adapt filters, allowing them to apply a different geometrical variant of the same filter to each location of the feature map. When evaluated on the Berkeley Segmentation contour detection dataset, our approach outperforms all competing approaches that do not utilize pre-training. Our results highlight the benefits of image-based regularization to deep networks.
Angiosarcoma of the heart: structural and ultrastructural study. (2005)

The light microscopy observation and immunohistochemical study underscore that is not easy to obtain information about the level of differentiation of this tumour. The presence of blood-filled lumina and the identification of typical markers of endothelial cells seems to indicate a well-differentiated nature. However, the ultrastructural findings seem to indicate a less differentiated nature.
Supplementary table 8 from Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3 (2023)

&lt;p&gt;Supplemental Table 8. Enrichment in regulatory regions for rs842357 and related SNPs&lt;/p&gt;
Abstract 18895: A Novel Gene Involved in Severe Neonatal Cardiomyopathy (2015)

Cardiomyopathies (CMP) in children are heterogeneous disorders of cardiac muscle with a relatively high incidence in infancy (8/100.000) as compared to older children (0.7/100.000). Beyond infancy, CMP is the most important indication for heart transplantation and transplantation free survival at 5 years after initial diagnosis is only 54%. Mutations in over 65 genes encoding sarcomeric, cytoskeletal and calcium-metabolizing proteins, cell-signaling molecules, and mitochondrial enzymes have been shown to cause CMPs. This has led to new recommendations for diagnostic evaluation and family screening incorporating genetic testing. However, present (targeted/custom based) diagnostic tests do not represent the whole spectrum of genetic etiologies and are leading to a correct diagnosis in just a subset of pediatric CMP patients. We present four children from two consanguineous families of Dutch and Moroccan descent with severe neonatal onset of CMP, ranging from lethal cardiomegaly with reduced contractility in three to severe left ventricular hypertrophy that remained stable in one child. A combined approach using homozygosity mapping and exome sequencing in both families identified a homozygous splice site variant resulting in exon skipping in the Dutch family, and a homozygous nonsense mutation in the Moroccan family within the same gene. This novel disease causing gene is implicated in the early differentiation of cardiomyocytes. Both variants were confirmed with Sanger sequencing and absent in large control populations. Previously published studies in a knockout mouse model demonstrated the functional role of this gene in CMPs. Additionally, we investigated the effect of the homozygous splice site mutation on the expression of different proteins at myocardial cell-cell junctions and myofibrils. These results point towards a role in intercalated disk remodeling. Electron microscopy- and protein expression studies on heart tissue of the patients are ongoing. Our findings add a new autosomal recessive gene to the list of genes already implicated in pediatric CMP, underscoring its genetic heterogeneity. Furthermore, our study indicates that the application of exome sequencing can improve the diagnostic yield in pediatric CMP.
Effect of Time Since Death on Multipathogen Molecular Test Results of Postmortem Specimens Collected Using Minimally Invasive Tissue Sampling Techniques (2021)

Results suggest that lung, liver, and blood specimens can be collected using MITS procedures up to 4 days after death in adequately preserved bodies. However, inconsistent pathogen detection in samples needs careful consideration before drawing definitive conclusions on the etiologic causes of death.
Sustained control of viremia following therapeutic immunization in chronically HIV-1-infected individuals (2006)

Our findings provide evidence that therapeutic immunization significantly impacts on HIV-1 replication. This translated into a decrease of up to 40% in the duration of exposure to antiretroviral drugs over 15 months of patients' follow-up.
meso,β‐Oligohaloporphyrins as Useful Synthetic Intermediates of Diphenylamine‐Fused Porphyrin and meso‐to‐meso β‐to‐β Doubly Butadiyne‐Bridged Diporphyrin (2015)

Abstract The chlorination of β‐halo or β,β‐dihaloporphyrins with 2‐chloro‐1,3‐bis(methoxycarbonyl)guanidine (Palau′Chlor) proceeded selectively at the neighboring unsubstituted meso position to afford meso,β‐dihalo or meso,β,β‐trihaloporphyrins. Such oligohaloporphyrins are useful platforms for constructing more‐elaborate porphyrin‐based extended π systems. For example, meso‐chloro‐β,β‐diiodoporphyrin participated in an efficient single‐step synthesis of a diphenylamine‐fused porphyrin. In addition, meso‐chloro‐β‐iodoporphyrin was transformed in stepwise fashion into an efficiently conjugated meso‐to‐meso,β‐to‐β doubly butadiyne‐linked porphyrin dimer, a system which was previously difficult to access without such haloporphyrin precursors.
Sexually transmitted infections and use of contraceptives in women living with HIV in Denmark – the SHADE cohort (2016)

The prevalence of STIs in WLWH in Denmark was low. The need for annual STI screening is questionable. Condoms were preferred contraceptives, especially in WLWH with an HIV-negative partner. In this cohort, 13 % of WLWH of reproductive age were at risk of unintended pregnancies due to lack of birth-control. Finally, in the subgroup of WLWH receiving both hormonal contraceptives and HAART possible drug-drug interactions could occur.
SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy (2019)

Abstract Background The crisis of Misidentified and contaminated cell lines have plagued the biological research community for decades. Some repositories and journals have heeded calls for mandatory authentication of human cell lines, yet misidentification of mouse cell lines has received little publicity despite their importance in sponsored research. Short tandem repeat (STR) profiling is the standard authentication method, but it may fail to distinguish cell lines derived from the same inbred strain of mice. Additionally, STR profiling does not reveal karyotypic changes that occur in some high-passage lines and may have functional consequences. Single nucleotide polymorphism (SNP) profiling has been suggested as a more accurate and versatile alternative to STR profiling; however, a high-throughput method for SNP-based authentication of mouse cell lines has not been described. Results We have developed computational methods (Cell Line Authentication by SNP Profiling, CLASP) for cell line authentication and copy number analysis based on a cost-efficient SNP array, and we provide a reference database of commonly used mouse strains and cell lines. We show that CLASP readily discriminates among cell lines of diverse taxonomic origins, including multiple cell lines derived from a single inbred strain, intercross or wild caught mouse. CLASP is also capable of detecting contaminants present at concentrations as low as 5%. Of the 99 cell lines we tested, 15 exhibited substantial divergence from the reported genetic background. In all cases, we were able to distinguish whether the authentication failure was due to misidentification (one cell line, Ba/F3), the presence of multiple strain backgrounds (five cell lines), contamination by other cells and/or the presence of aneuploid chromosomes (nine cell lines). Conclusions Misidentification and contamination of mouse cell lines is potentially as widespread as it is in human cell culture. This may have substantial implications for studies that are dependent on the expected background of their cell cultures. Laboratories can mitigate these risks by regular authentication of their cell cultures. Our results demonstrate that SNP array profiling is an effective method to combat cell line misidentification.
5G mmWave Cooperative Positioning and Mapping using Multi-Model PHD Filter and Map Fusion (2019)

5G millimeter wave (mmWave) signals can enable accurate positioning in vehicular networks when the base station and vehicles are equipped with large antenna arrays. However, radio-based positioning suffers from multipath signals generated by different types of objects in the physical environment. Multipath can be turned into a benefit, by building up a radio map (comprising the number of objects, object type, and object state) and using this map to exploit all available signal paths for positioning. We propose a new method for cooperative vehicle positioning and mapping of the radio environment, comprising a multiple-model probability hypothesis density filter and a map fusion routine, which is able to consider different types of objects and different fields of views. Simulation results demonstrate the performance of the proposed method.
ChemInform Abstract: Copper‐Catalyzed Silylation of Cyclopropenes Using (Trifluoromethyl)trimethylsilane. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.