gebhart/patrepeval huggingface dataset:
A Hierarchical Bayesian Choice Model with Visibility (2014)

We extend the standard choice model of multinomial logit model (MLM) into a hierarchical Bayesian model to simultaneously estimate the preferences of customers and the visibility of items from purchasing history. We say that an item has high visibility when customers well consider that item as a candidate before making a choice. We design two algorithms for estimating the parameters of the proposed choice model. One algorithm estimates the posterior distribution with the Gibbs sampling, and the other approximately performs the maximum a posteriori estimation. Our experimental results show that we can estimate the preferences of customers from their purchasing history without the prior knowledge of the choice set. The existing approaches to estimating the preferences of customers rely on the explicit knowledge of the choice set.
Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control (2016)

Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.
Misting of printing inks (1980)

The initial objective of NAPIM's misting project at Lehigh University is to develop a viable standard test method for evaluating the misting tendencies of printing inks. An ensuing objective will be to identify the ink characteristics responsible for misting. Development of such information is expected to uncover approaches for minimizing misting problems.
AE: An Asymmetric Extremum content defined chunking algorithm for fast and bandwidth-efficient data deduplication (2015)

Data deduplication, a space-efficient and bandwidth-saving technology, plays an important role in bandwidth-efficient data transmission in various data-intensive network and cloud applications. Rabin-based and MAXP-based Content-Defined Chunking (CDC) algorithms, while robust in finding suitable cut-points for chunk-level redundancy elimination, face the key challenges of (1) low chunking throughput that renders the chunking stage the deduplication performance bottleneck and (2) large chunk-size variance that decreases deduplication efficiency. To address these challenges, this paper proposes a new CDC algorithm called the Asymmetric Extremum (AE) algorithm. The main idea behind AE is based on the observation that the extreme value in an asymmetric local range is not likely to be replaced by a new extreme value in dealing with the boundaries-shift problem, which motivates AE's use of asymmetric (rather than symmetric as in MAXP) local range to identify cut-points and simultaneously achieve high chunking throughput and low chunk-size variance. As a result, AE simultaneously addresses the problems of low chunking throughput in MAXP and Rabin and high chunk-size variance in Rabin. The experimental results based on four real-world datasets show that AE improves the throughput performance of the state-of-the-art CDC algorithms by 3x while attaining comparable or higher deduplication efficiency.
Modeling and Feedback of Turbulence Hazards Based on Automated Real-Time Pilot Reports (2009)

In this paper, we present an Air Traffic Management (ATM) impact model based on the collection of real-time Turbulence Auto-PIREP System (TAPS) reports measuring turbulence severity. The approach is applicable to all forms of turbulence hazards, including Convective Induced Turbulence (CIT), Clear Air Turbulence (CAT), and Mountain Wave Turbulence (MWT). We analyze TAPS data from aircraft flying in and around convective activity in order to study where CIT resides relative to hazardous convective weather cells. CIT may be both collocated with severe convective activity as well as nearby it. Thus, pilots often do not know exactly where CIT is located, so they may fly through it while avoiding hazardous convective weather cells. Finally, we present a model for hazard avoidance that can be used as a feedback mechanism for aircraft nearby a lead aircraft that enters into CIT. This weather avoidance guidance is useful for avoiding both the convective weather cells and known CIT in and around a region of interest.
Drastic initial response and subsequent response to two ALK inhibitors in a patient with a highly aggressive ALK-rearranged inflammatory myofibroblastic tumor arising in the pleural cavity (2016)

A 57-year-old male current smoker was diagnosed with an aggressive variant of ALK-rearranged inflammatory myofibroblastic tumor (IMT) arising in the pleural cavity. First line treatment with ASP3026 was initiated at a dose of 125mg once daily. A follow-up CT scan revealed drastic regression of the pleural lesion. After disease progression with ASP3026 treatment, LDK378 (ceritinib) was initiated at a dose of 750mg once daily. A follow-up CT scan revealed a second drastic regression of the pleural lesion. Furthermore, it is noteworthy that this case represents the use of serum hyaluronan levels to assist in monitoring of treatment efficacy in an IMT. Herein, we present the first case of a patient with a highly aggressive ALK-rearranged IMT arising in the pleural cavity, who showed both initial and subsequent drastic response to two ALK inhibitors while being monitored for serum hyaluronan.
Identification of QTLs for Resistance to Sclerotinia Stem Rot and BnaC.IGMT5.a as a Candidate Gene of the Major Resistant QTL SRC6 in Brassica napus (2013)

Stem rot caused by Sclerotinia sclerotiorum in many important dicotyledonous crops, including oilseed rape (Brassica napus), is one of the most devastating fungal diseases and imposes huge yield loss each year worldwide. Currently, breeding for Sclerotinia resistance in B. napus, as in other crops, can only rely on germplasms with quantitative resistance genes. Thus, the identification of quantitative trait locus (QTL) for S. sclerotiorum resistance/tolerance in this crop holds immediate promise for the genetic improvement of the disease resistance. In this study, ten QTLs for stem resistance (SR) at the mature plant stage and three QTLs for leaf resistance (LR) at the seedling stage in multiple environments were mapped on nine linkage groups (LGs) of a whole genome map for B. napus constructed with SSR markers. Two major QTLs, LRA9 on LG A9 and SRC6 on LG C6, were repeatedly detected across all environments and explained 8.54-15.86% and 29.01%-32.61% of the phenotypic variations, respectively. Genotypes containing resistant SRC6 or LRA9 allele showed a significant reduction in disease lesion after pathogen infection. Comparative mapping with Arabidopsis and data mining from previous gene profiling experiments identified that the Arabidopsis homologous gene of IGMT5 (At1g76790) was related to the SRC6 locus. Four copies of the IGMT5 gene in B. napus were isolated through homologous cloning, among which, only BnaC.IGMT5.a showed a polymorphism between parental lines and can be associated with the SRC6. Furthermore, two parental lines exhibited a differential expression pattern of the BnaC.IGMT5.a gene in responding to pathogen inoculation. Thus, our data suggested that BnaC.IGMT5.a was very likely a candidate gene of this major resistance QTL.
Towards privacy-preserving integration of distributed heterogeneous data (2008)

More and more applications rely heavily on large amounts of data in the distributed storages collected over time or produced by large scale scientific experiments or simulations. An important fact is that many organizations collect, store, and use various types of information about individuals. In consequence, such data sharing is subject to constraints imposed by privacy of individuals or data subjects as well as data confidentiality of institutions or data providers. Given a query spanning multiple databases, it should be executed transparently and efficiently. And most importantly, the results should not contain individually identifiable information and institutions should not reveal their databases to each other apart from the query results. In this paper, we propose a distributed anonymization protocol that allows independent data providers to build a virtual anonymized database from horizontally partitioned databases, and a secure query protocol that allows clients to query those virtual databases. We also propose a distributed data sharing and integration architecture for querying these distributed heterogeneous and possibly private databases. Our system provides efficient and scalable privacy-preserving query execution interface that integrates data seamlessly and transparently.
Exploring Cellular Activity of Locked Nucleic Acid-modified Triplex-forming Oligonucleotides and Defining Its Molecular Basis (2005)

Triplex-forming oligonucleotides (TFOs), as DNA-binding molecules that recognize specific sequences, offer unique potential for the understanding of processes occurring on DNA and associated functions. They are also powerful DNA recognition elements for the positioning of ubiquitous molecules acting on DNA, such as anticancer drugs. A prerequisite for further development of DNA code-reading molecules including TFOs is their ability to form a complex in a cellular context: their binding affinities must be comparable to those of DNA-associated proteins. To reach this goal, chemically modified TFOs must be developed. In this work, we present triplex-forming properties (kinetics and thermodynamics) and cellular activity of G-containing locked nucleic acid-modified TFOs (TFO/LNAs). In conditions simulating physiological ones, these TFO/LNAs strongly enhanced triplex stability compared with the non-modified TFO or with the pyrimidine TFO/LNA directed against the same oligopyrimidine.oligopurine sequence, mainly by decreasing the dissociation rate constant and conferring an entropic gain. We provide evidence of their biological activity by a triplex-based mechanism, in vitro and in a cellular context, under conditions in which the parent phosphodiester oligonucleotide did not exhibit any inhibitory effect.
Intravenous Itraconazole followed by Oral Itraconazole for the Treatment of Amphotericin-B-Refractory Invasive Pulmonary Aspergillosis (2003)

The efficacy and safety of 2 weeks of intravenous itraconazole (200 mg twice daily for 2 days, then 200 mg once daily for 12 days) followed by 12 weeks of oral itraconazole capsules 200 mg twice daily were evaluated in a multicentre, open trial in 31 immunocompromised patients with invasive pulmonary aspergillosis (IPA). We report on a subset of 21 patients who had amphotericin-B-refractory IPA. All patients had haematological malignancies, 10 patients had failed prophylaxis, 12 patients had failed empirical therapy and 2 patients had failed treatment of confirmed infection with amphotericin B. By the second day of treatment, all patients assessed (n = 12) had trough plasma concentrations of itraconazole greater than 250 ng/ml. Mean trough plasma concentrations increased throughout the intravenous and oral treatment periods. Of the 10 patients who completed the 14 weeks of therapy, 9 (90%) had a complete or partial response and the remaining patient had stable disease. Overall, 11 of the 21 patients (52%) had a complete or partial response at their last assessment and three additional patients had stable disease. During intravenous treatment, 18 patients (86%) experienced adverse events; during oral treatment, 11 patients (52%) experienced adverse events. Most adverse events were not related to itraconazole treatment and all were expected in this patient population. In conclusion, intravenous itraconazole followed by oral itraconazole is an effective and well-tolerated treatment for amphotericin-B-refractory IPA.
Electrical characteristics of selenium-treated GaAs MIS Schottky diodes (1993)

The author has investigated the effect of selenium treatment of GaAs on the metal-insulator-semiconductor (MIS) Schottky diode characteristics. The results show that the surface-state density and trap density at the interface decrease. This results in decrease in the barrier height and reverse current. The treated diodes showed little aging effect. These observations can be explained using the formation of arsenic selenium and selenium-selenium bonds at the surface and in the thin layer next to the surface within the GaAs.
Wander in the magic of the labyrinth : on the farm (2012)

One way in, one way out - thus is the way of the labyrinth. And this is more or less the philosophy that is followed by Doolhof Wine Estate - there is only one road that leads in and out of the estate and there is only one way of doing things: the best way.
Use of Psoralens for Covalent Immobilization of Biomolecules in Solid Phase Assays (1994)

The ability of compounds to adsorb passively to hydrophobic polymer surfaces composed of, e.g., polystyrene generally is restricted to limited types of molecules such as proteins. Some proteins, many peptides, polysaccharides, oligonucleotides, and small molecules as well as pro- and eucaryotic cells cannot adsorb directly to such surfaces. Also, solid phase adsorbed antigens, antibodies, or gene probes may not be recognized by its corresponding ligand due to denaturation or steric hindrance of the molecular tertiary structure. Covalent binding, on the other hand, orientates all immobilized compounds in a defined way on the solid phase, thereby exposing the interacting sites on the enzymes, antibodies, gene probes, etc. Here we describe a method for modifying a polymer surface by contacting the polymer with derivatives of psoralen under irradiation with long-wavelength UV light. The psoralen derivatives were immobilized covalently on the polymer surface by this process. The psoralen molecules was conjugated to appropriate chemical linkers, incubated in aqueous solutions, and irradiated with UV light. This resulted in solid phase introduction of functional groups such as, e.g., amino groups on the polystyrene surface. The functional groups could subsequently be used for immobilization of biomolecules using conventional cross-linker technology. The method only involved premodification of the psoralens to be immobilized whereas no pretreatment of the polymer was required. Psoralen modified microtiter plates seems to have future application for the development of solid phase hybridization and immunoassays.
Bifunctional Antibody Retargeting In Vivo-Activated T Lymphocytes: Simplifying Clinical Application (1995)

For antitumor x anti-CD3 bifunctional antibody (BFA) therapy to be clinically relevant in solid tumors, activated lymphocytes must be present within tumors. Toward that end, three uniquely different in vivo activation approaches were investigated in a p97 human antigen expressing syngeneic murine melanoma model. beta-Glucan (200 micrograms), staphylococcal enterotoxin B (SEB) (50 micrograms), and F(ab')2 BFA (10 micrograms) were tested for their ability to activate lymphocytes, neutralize pulmonary metastases, and treat established tumors. Systemic activation, measured as the ability of splenocytes to lyse tumor cells in vitro in the presence of BFA, was enhanced by the in vivo administration of SEB but not by beta-glucan or F(ab')2 BFA. Despite lacking a systemic effect, F(ab')2 BFA increased both direct and BFA-mediated cytotoxicity in fresh tumor infiltrating lymphocytes. beta-Glucan did not increase systemic or intratumor T cell activation. However, it significantly enhanced the ability of splenocytes to lyse NK-sensitive YAC-1 cells. When tested in a pulmonary metastases model, all three forms of immune modulation combined with F(ab')2 BFA significantly reduced the number of metastases. BFA were more effective at tumor neutralization when combined with SEB compared with adoptively transferred, in vitro-activated splenocytes. These studies demonstrate that immune modulators when combined with F(ab')2 BFA can provide effective antitumor therapy. Several clinical obstacles may be overcome by the application of these reagents.
A Novel 125l Radioimmunoassay for the Analysis of  9-Tetrahydrocannabinol and its Metabolites in Human Body Fluids (1984)

A cannabinoid radioimmunoassay (RIA) that detects some of the major delta 9-THC metabolites is developed and evaluated for use in forensic science. It incorporates a novel 125I radiotracer, is sensitive, reliable, relatively quick, and simple to use. The RIA uses a commercially available antiserum and detects a number of cannabinoid metabolites, including delta 9-THC-11-oic acid and its glucuronide conjugate in biological fluids. The method was successfully applied to the analysis of blood and urine samples submitted for forensic analysis.
Critical Assessment of Implantable Drug Delivery Devices in Glaucoma Management (2013)

Glaucoma is a group of heterogeneous disorders involving progressive optic neuropathy that can culminate into visual impairment and irreversible blindness. Effective therapeutic interventions must address underlying vulnerability of retinal ganglion cells (RGCs) to degeneration in conjunction with correcting other associated risk factors (such as elevated intraocular pressure). However, realization of therapeutic outcomes is heavily dependent on suitable delivery system that can overcome myriads of anatomical and physiological barriers to intraocular drug delivery. Development of clinically viable sustained release systems in glaucoma is a widely recognized unmet need. In this regard, implantable delivery systems may relieve the burden of chronic drug administration while potentially ensuring high intraocular drug bioavailability. Presently there are no FDA-approved implantable drug delivery devices for glaucoma even though there are several ongoing clinical studies. The paper critically assessed the prospects of polymeric implantable delivery systems in glaucoma while identifying factors that can dictate (a) patient tolerability and acceptance, (b) drug stability and drug release profiles, (c) therapeutic efficacy, and (d) toxicity and biocompatibility. The information gathered could be useful in future research and development efforts on implantable delivery systems in glaucoma.
Decoding the signaling profile of hematopoietic progenitor kinase 1 (HPK1) in innate immunity: A proteomic approach (2022)

Signaling via β<sub>2</sub> integrins (CD11/CD18) as well as TCRs and BCRs involves similar pathways. However, the activation of the same signaling molecule can result in opposing effects. One such example is the hematopoietic progenitor kinase 1 (HPK1), which negatively regulates T and B cell activation but enforces neutrophil adhesion via β<sub>2</sub> integrins. This difference may be defined by specific HPK1 interacting networks in different leukocyte subsets which have already been described in the adaptive immune system. Here, we set out to identify interacting proteins of HPK1 in neutrophil-like differentiated HL-60 cells exposed to immobilized fibrinogen and left nonactivated or Mn<sup>2+</sup> -activated to allow β<sub>2</sub> integrin-dependent adhesion. Co-IP experiments followed by mass spectrometry led to the identification of 115 HPK1-interacting proteins. A total of 58 proteins were found only in nonactivated cells and 39 proteins only in Mn<sup>2+</sup> -activated adherent cells. From these results, we decoded a pre-existing signaling cluster of HPK1 in nonactivated cells encompassing proteins essential for β<sub>2</sub> integrin-mediated signaling during neutrophil trafficking, namely DNAX-activation protein 12 (DAP12), spleen tyrosine kinase (Syk), and Rac1. Thus, our study provides novel insights into the complex architecture of the signaling processes during neutrophil activation and the complex signaling profile of HPK1 in leukocytes.
An Anti-Programmed Death-1 Antibody (αPD-1) Fusion Protein That Self-Assembles into a Multivalent and Functional αPD-1 Nanoparticle (2017)

Cancer immune checkpoint therapy has achieved remarkable clinical successes in various cancers. However, current immune checkpoint inhibitors block the checkpoint of not only the immune cells that are important to cancer therapy but also the immune cells that are irrelevant to the therapy. Such an indiscriminate blockade limits the efficacy and causes the autoimmune toxicity of the therapy. It might be beneficial to use a carrier to target immune checkpoint inhibitors to cancer-reactive immune cells. Here, we explore a method to load the inhibitors into carriers. We used the anti-programmed death-1 antibody (αPD-1) as a model immune checkpoint inhibitor. First, we generated a recombinant single-chain variable fragment (scFv) of αPD-1. Then, we designed and generated a fusion protein consisting of the scFv and an amphiphilic immune-tolerant elastin-like polypeptide (iTEP). Because of the amphiphilic iTEP, the fusion was able to self-assemble into a nanoparticle (NP). The NP was proved to block the PD-1 immune checkpoint in vitro and in vivo. Particularly, the NP exacerbated diabetes development in nonobese diabetic mice as effectively as natural, intact αPD-1. In summary, we successfully expressed αPD-1 as a recombinant protein and linked αPD-1 to a NP, which lays a foundation to develop a delivery system to target αPD-1 to a subpopulation of immune cells.
In vitro synergy testing of novel antimicrobial combination therapies against Neisseria gonorrhoeae (2014)

Combinations of ceftriaxone plus rifampicin, gentamicin or fosfomycin may warrant further clinical investigation as treatments for gonorrhoea. Using the Etest for synergy testing is a viable method that has practical advantages over agar dilution.
Analysis of and compensation for non-ideal RoF links in DAS [Coordinated and Distributed MIMO] (2010)

Distributed antenna systems have been found to be an elegant solution for the problems arising in high-data-rate wireless communication, particularly in large service areas. This article considers radio over fiber links as an essential part of the DAS, connecting the central unit with the remote antenna units. In particular, we analyze and discuss delays and nonlinearities stemming from the RoF links. In addition, we study the compensation for these impairments. Our studies indicate that the RoF links are a viable and cost-effective solution for implementing the DAS, although some of the RoF link non-idealities require compensation.