gebhart/patrepeval huggingface dataset:
Intestinal spirochaetes (Brachyspiraspp.) colonizing flocks of layer and breeder chickens in Malaysia (2014)

Avian intestinal spirochaetosis causes problems including delayed onset of lay and wet litter in adult chickens, and results from colonization of the caecae/rectum with pathogenic intestinal spirochaetes (genus Brachyspira). Because avian intestinal spirochaetosis has not previously been studied in South East Asia, this investigation was undertaken in Malaysia. Faecal samples were collected from 25 farms and a questionnaire was administered. Brachyspira species were detected by polymerase chain reaction in 198 of 500 (39%) faecal samples from 20 (80%) farms, including 16 (94%) layer and four (50%) breeder farms. Pathogenic Brachyspira pilosicoli was identified in five (29%) layer and two (25%) breeder farms whilst pathogenic Brachyspira intermedia was detected in nine (53%) layer and one (12.5%) of the breeder farms. Twelve (80%) layer farms had egg production problems and 11 (92%) were positive for Brachyspira: three (25%) for B. pilosicoli and six (50%) for B. intermedia. Of three breeder farms with egg production problems, one was colonized with B. pilosicoli. Three of ten layer farms with wet litter were positive for B. pilosicoli and six for B. intermedia. Of four breeder farms with wet litter, one was colonized with B. pilosicoli and one with B. intermedia. No significant associations were found between colonization and reduced egg production or wet litter, perhaps because so many flocks were colonized. A significant association (P = 0.041) occurred between a high prevalence of colonization and faecal staining of eggs. There were significant positive associations between open-sided housing (P = 0.006), and flocks aged >40 weeks (P < 0.001) and colonization by pathogenic species.
EML4-ALK fusion gene and sensitivity to an ALK kinase inhibitor in lung cancer (2008)

2373 The EML4-ALK fusion gene, resulting from an inversion on chromosome 2p, has recently been detected in ~7% of Japanese non-small cell lung cancers (NSCLC). This genetic alteration was also transforming in vitro and in vivo . In the current study we examined the frequency of EML4-ALK in NSCLCs (n=305) derived from US and Korean patients and in NSCLC cell lines (n= 83). We detected 4 different variants of EML4-ALK using RT-PCR in 8 (3%) NSCLC (2/138 (1.5%) from US NSCLC patients; 6/167 (3.6%) from Korean patients) and in 3/83 (3.6%) NSCLC cell lines. All EML4-ALK containing tumors and cell lines were adenocarcinomas and occurred more frequently in NSCLC patients who were never or light ( EML4-ALK inversion. Despite inhibiting ALK phosphorylation in all 3 cell lines, the growth of only 1 of the 3 cell lines, H3122, was inhibited by NVP-TAE684 and this was accompanied by significant apoptosis. In the other 2 EML4-ALK containing cell lines, unlike in H3122, inhibition of ALK phosphorylation led to no or only partial inhibition of AKT, STAT3 or ERK 1/2 phosphorylation. These studies suggest that ALK inhibitors may be potentially effective therapies for a subset of lung cancers harbouring the EML4-ALK inversion and further support their clinical development
B-MIND: MOR208 plus bendamustine (BEN) versus rituximab (RTX) plus BEN in patients with relapsed or refractory (R-R) diffuse large B-cell lymphoma (DLBCL): An open-label, randomized phase II/III trial. (2017)

TPS7571 Background: Patients ineligible for stem cell transplantation (SCT) or who relapse after SCT, and those who fail to respond to second-line or salvage chemotherapy, represent an unmet medical need for which new therapeutic strategies are required. MOR208 is a novel Fc-enhanced, humanized, monoclonal antibody directed against CD19. Significant single-agent activity of MOR208 in patients with R-R DLBCL (Jurczak et al., J Clin Oncol 34, 2016 [suppl; abstr 7545]) and enhancement of MOR208-mediated cytotoxicity by BEN in preclinical studies, provide a strong rationale to study MOR208 + BEN in patients with R-R DLBCL. Methods: B-MIND is a randomized (1:1), two-arm, multicenter, open-label, adaptive design, phase II/III study of MOR208 + BEN vs RTX + BEN in adult patients with histologically confirmed DLBCL who have relapsed after or are refractory to 1 to 3 prior lines of therapy and who are not candidates for high-dose chemotherapy and autologous SCT. At least 1 prior therapy line must have included a CD20-targeted therapy. Other key inclusion criteria: age ≥18 years; measurable disease; availability of tumor tissue for central pathology review; ECOG 0–2, and adequate major organ systems function. Key exclusion criteria: primary refractory DLBCL; central nervous system involvement, and known double/triple hit DLBCL genetics. The safety of the combination will be assessed in an initial phase II evaluation. Treatment will comprise 6 cycles of MOR208 (12 mg/kg IV) + BEN (90 mg/m 2 IV) or RTX 375 mg/m 2 IV + BEN. Patients achieving a response after cycle 6 will continue to receive antibody treatment for up to 18 additional cycles. Primary endpoint: progression-free survival (PFS); secondary endpoints include: best overall response, overall survival, safety, quality of life, immunogenicity and pharmacokinetics. Enrollment of 330 patients is anticipated in Europe, US and Asia-Pacific countries. Fourteen patients have been randomized to date. Clinical trial information: NCT02763319.
Accelerated discovery of 3D printing materials using data-driven multiobjective optimization (2021)

Additive manufacturing has become one of the forefront technologies in fabrication, enabling products impossible to manufacture before. Although many materials exist for additive manufacturing, most suffer from performance trade-offs. Current materials are designed with inefficient human-driven intuition-based methods, leaving them short of optimal solutions. We propose a machine learning approach to accelerating the discovery of additive manufacturing materials with optimal trade-offs in mechanical performance. A multiobjective optimization algorithm automatically guides the experimental design by proposing how to mix primary formulations to create better performing materials. The algorithm is coupled with a semiautonomous fabrication platform to substantially reduce the number of performed experiments and overall time to solution. Without prior knowledge of the primary formulations, the proposed methodology autonomously uncovers 12 optimal formulations and enlarges the discovered performance space 288 times after only 30 experimental iterations. This methodology could be easily generalized to other material design systems and enable automated discovery.
Identification of Bacterial Plant Pathogens Using Multilocus Polymerase Chain Reaction/Electrospray Ionization-Mass Spectrometry (2008)

Polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS, previously known as "TIGER") utilizes PCR with broad-range primers to amplify products from a wide array of organisms within a taxonomic group, followed by analysis of PCR amplicons using mass spectrometry. Computer analysis of precise masses allows for calculations of base compositions for the broad-range PCR products, which can then be compared to a database for identification. PCR/ESI-MS has the benefits of PCR in sensitivity and high-throughput capacity, but also has the distinct advantage of being able to detect and identify organisms with no prior characterization or sequence data. Existing broad range PCR primers, designed with an emphasis on human pathogens, were tested for their ability to amplify DNA of well characterized phytobacterial strains, as well as to populate the existing PCR/ESI-MS bacterial database with base counts. In a blinded panel study, PCR/ESI-MS successfully identified 93% of unknown bacterial DNAs to the genus level and 73% to the species/subspecies level. Additionally, PCR/ESI-MS was capable of detecting and identifying multiple bacteria within the same sample. The sensitivity of PCR/ESI-MS was consistent with other PCR based assays, and the specificity varied depending on the bacterial species. Preliminary tests with real life samples demonstrate a high potential for using PCR/ESI-MS systems for agricultural diagnostic applications.
Concordance of experimentally mapped or predicted Z-DNA sites with positions of selected alternating purine-pyrimidine tracts (1985)

The recent electronmicroscopic and biochemical mapping of Z-DNA sites in phi X174, SV40, pBR322 and PM2 DNAs has been used to determine two sets of criteria for identification of potential Z-DNA sequences in natural DNA genomes. The prediction of potential Z-DNA tracts and corresponding statistical analysis of their occurrence have been made on a sample of 14 DNA genomes. Alternating purine and pyrimidine tracts longer than 5 base pairs in length and their clusters (quasi alternating fragments) in the 14 genomes studied are under-represented compared to the expectation from corresponding random sequences. The fragments [d(G X C)]n and [d(C X G)]n (n greater than or equal to 3) in general do not occur in circular DNA genomes and are under-represented in the linear DNAs of phages lambda and T7, whereas in linear genomes of adenoviruses they are strongly over-represented. With minor exceptions, potential Z-DNA sites are also under-represented compared to random sequences. In the 14 genomes studied, predicted Z-DNA tracts occur in non-coding as well as in protein coding regions. The predicted Z-DNA sites in phi X174, SV40, pBR322 and PM2 correspond well with those mapped experimentally. A complete listing together with a compact graphical representation of alternating purine-pyrimidine fragments and their Z-forming potential are presented.
1.55 μm traveling-wave amplification photodetector (2003)

We demonstrate a novel InP-based ridge-waveguide photodetector with monolithically integrated multiple-quantum well amplification layers. Performance limitations are analyzed using advanced device simulation and design optimizations are proposed.
Private Predictive Analysis on Encrypted Medical Data. (2014)

Increasingly, confidential medical records are being stored in data centers hosted by hospitals or large companies. As sophisticated algorithms for predictive analysis on medical data continue to be developed, it is likely that, in the future, more and more computation will be done on private patient data. While encryption provides a tool for assuring the privacy of medical information, it limits the functionality for operating on such data. Conventional encryption methods used today provide only very restricted possibilities or none at all to operate on encrypted data without decrypting it first. Homomorphic encryption provides a tool for handling such computations on encrypted data, without decrypting the data, and without even needing the decryption key. In this paper, we discuss possible application scenarios for homomorphic encryption in order to ensure privacy of sensitive medical data. We describe how to privately conduct predictive analysis tasks on encrypted data using homomorphic encryption. As a proof of concept, we present a working implementation of a prediction service running in the cloud (hosted on Microsoft’s Windows Azure), which takes as input private encrypted health data, and returns the probability for suffering cardiovascular disease in encrypted form. Since the cloud service uses homomorphic encryption, it makes this prediction while handling only encrypted data, learning nothing about the submitted confidential medical data.
Energy Aware Provisioning in Solar Powered WLAN Mesh Networks (2008)

WLAN mesh networks are often installed to provide wireless coverage for temporary events. In these types of networks, the WLAN mesh nodes can sometimes be operated using an energy sustainable source such as solar power. Resource provisioning consists of pre-assigning each node with a solar panel and battery combination that is sufficient to prevent node outage for the duration of the deployment. This is done by assuming a temporal load profile for each node, which is then used to perform the assignment using historical solar insolation data for the desired deployment location. Unfortunately, this methodology cannot take into account the state dependencies which occur when the network uses energy aware routing, and therefore the system may be over-provisioned. In this paper we propose a methodology for WLAN mesh node resource assignment that incorporates energy aware routing into the assignment algorithm. The problem consists of determining a network-wide minimum cost resource assignment subject to satisfying the input load profile. A genetic algorithm (GA) has been developed for this purpose. Our results show the large resource savings that energy aware resource assignment can achieve when compared to that done using the conventional methodology. We also study the competitive ratio of both resource assignment schemes and show that for small traffic overloading, energy aware routing performs better than shortest path routing in networks which are provisioned using the proposed methodology.
Data from Heterochromatin Protein 1α Mediates Development and Aggressiveness of Neuroendocrine Prostate Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer arising mostly from adenocarcinoma via neuroendocrine transdifferentiation following androgen deprivation therapy. Mechanisms contributing to both NEPC development and its aggressiveness remain elusive. In light of the fact that hyperchromatic nuclei are a distinguishing histopathologic feature of NEPC, we utilized transcriptomic analyses of our patient-derived xenograft (PDX) models, multiple clinical cohorts, and genetically engineered mouse models to identify 36 heterochromatin-related genes that are significantly enriched in NEPC. Longitudinal analysis using our unique, first-in-field PDX model of adenocarcinoma-to-NEPC transdifferentiation revealed that, among those 36 heterochromatin-related genes, heterochromatin protein 1α (HP1α) expression increased early and steadily during NEPC development and remained elevated in the developed NEPC tumor. Its elevated expression was further confirmed in multiple PDX and clinical NEPC samples. &lt;i&gt;HP1α&lt;/i&gt; knockdown in the NCI-H660 NEPC cell line inhibited proliferation, ablated colony formation, and induced apoptotic cell death, ultimately leading to tumor growth arrest. Its ectopic expression significantly promoted NE transdifferentiation in adenocarcinoma cells subjected to androgen deprivation treatment. Mechanistically, HP1α reduced expression of androgen receptor and RE1 silencing transcription factor and enriched the repressive trimethylated histone H3 at Lys9 mark on their respective gene promoters. These observations indicate a novel mechanism underlying NEPC development mediated by abnormally expressed heterochromatin genes, with HP1α as an early functional mediator and a potential therapeutic target for NEPC prevention and management.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; Heterochromatin proteins play a fundamental role in NEPC, illuminating new therapeutic targets for this aggressive disease. &lt;i&gt;Cancer Res; 78(10); 2691–704. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Cloning and Characterization of the Glucosidase II Alpha Subunit Gene of Trichoderma reesei : a Frameshift Mutation Results in the Aberrant Glycosylation Profile of the Hypercellulolytic Strain Rut-C30 (2005)

We describe isolation and characterization of the gene encoding the glucosidase II alpha subunit (GIIalpha) of the industrially important fungus Trichoderma reesei. This subunit is the catalytic part of the glucosidase II heterodimeric enzyme involved in the structural modification within the endoplasmic reticulum (ER) of N-linked oligosaccharides present on glycoproteins. The gene encoding GIIalpha (gls2alpha) in the hypercellulolytic strain Rut-C30 contains a frameshift mutation resulting in a truncated gene product. Based on the peculiar monoglucosylated N-glycan pattern on proteins produced by the strain, we concluded that the truncated protein can still hydrolyze the first alpha-1,3-linked glucose residue but not the innermost alpha-1,3-linked glucose residue from the Glc2Man9GlcNAc2 N-glycan ER structure. Transformation of the Rut-C30 strain with a repaired T. reesei gls2alpha gene changed the glycosylation profile significantly, decreasing the amount of monoglucosylated structures and increasing the amount of high-mannose N-glycans. Full conversion to high-mannose carbohydrates was not obtained, and this was probably due to competition between the endogenous mutant subunit and the introduced wild-type GIIalpha protein. Since glucosidase II is also involved in the ER quality control of nascent polypeptide chains, its transcriptional regulation was studied in a strain producing recombinant tissue plasminogen activator (tPA) and in cultures treated with the stress agents dithiothreitol (DTT) and brefeldin A (BFA), which are known to block protein transport and to induce the unfolded protein response. While the mRNA levels were clearly upregulated upon tPA production or BFA treatment, no such enhancement was observed after DTT addition.
Early Circulating Tumour DNA Variations Predict Tumour Response in Melanoma Patients Treated with Immunotherapy (2018)

Antibodies targeting immune checkpoints were recently approved for metastatic melanoma. However, not all patients will respond to the treatment and some will experience grade III-IV immune-related adverse events. Therefore, early identification of non-responder patients would greatly aid clinical practice. Detection of circulating tumour DNA (ctDNA) is a non-invasive approach to monitor tumour response. Digital droplet PCR was used to quantify BRAF and NRAS mutations in the plasma of patients with metastatic melanoma treated with immunotherapy. In 16 patients, ctDNA variations mirrored tumour response (p = 0.034) and ctDNA augmentation during follow-up detected tumour progression with 100% specificity. In 13 patients, early ctDNA variation was associated with clinician decision at first evaluation (p = 0.0046), and early ctDNA increase with shorter progression-free survival (median 21 vs. 145 days; p = 0.001). Monitoring ctDNA variations early during immunotherapy may help clinicians rapidly to discriminate non-responder patients, allow early adaptation of therapeutic strategies, and reduce exposure to ineffective, expensive treatment.
Constant impedance scaling paradigm for interconnect synthesis (2006)

On-chip global interconnects perceived as performance limiters for continued scaling of integrated circuits in nano-CMOS regimes highlight the importance of their proper design and optimization. A constant impedance scaling paradigm is proposed for systematic synthesis of complete interconnects physical parameters from system level performance metrics such as delay, power and wiring density. The methodology is illustrated for different system level targets and optimal physical parameters are deduced.
Size Distribution Change of Titania Nano-Particle Agglomerates Generated by Gas Phase Reaction, Agglomeration, and Sintering (2001)

In the manufacturing of nanometer-sized material particlulates by aerosol gas-to-particle conversion processes, it is important to analyze how the gas-phase chemical reaction, nucleation, agglomeration, and sintering rates control the size distribution and morphology of particles. In this study, titania particles were produced experimentally by the thermal decomposition of titanium tetraisopropoxide (TTIP) and oxidation of titanium tetrachloride (TiCl 4 ) using a laminar flow aerosol reactor. The effect of reaction temperature on the size and morphology of the generated particles was investigated under various conditions. The size distributions of agglomerates were measured using a DMA/CNC system. The size distributions of primary particles were measured using TEM pictures of the agglomerates sampled by a thermophoretic aerosol sampler. In order to model the growth of both agglomerates and primary particles simultaneously, a two-dimensional discrete-sectional representation of the size distribution was employed, solving the aerosol general dynamic equation for chemical reaction, agglomeration, and sintering. Qualitative agreement between the experimentally observed results and the simulation are satisfactory for the large variations in reactor temperature explored.
Evaluation of inertial measurement units as a novel method for kinematic gait evaluation in dogs (2016)

Canine sagittal plane motion data acquisition with IMU is feasible, and optically acquired and IMU acquired sagittal plane kinematics had good correlation. This technology allows data acquisition outside the gait laboratory and may provide an alternative to optical kinematic gait analysis for the carpal, tarsal, stifle, and hip joints in the dog. Further investigation into this technology is indicated.
Synthesis and substance P receptor binding activity of androstano[3,2-b]pyrimido[1,2-a]benzimidazoles (1992)

Several heterosteroids containing a dihydroethisterone skeleton were prepared and shown to displace substance P in a receptor binding assay. Further biochemical (kinetic and Scatchard analyses) and pharmacological evaluation (substance P-induced plasma extravasation and salivation in the rat) of a representative example in this series (5a) established that these compounds are competitive antagonists at the substance P receptor.
Thermal analysis of amorphous oxide thin-film transistor degraded by combination of joule heating and hot carrier effect (2013)

Stability is the most crucial issue in the fabrication of oxide thin-film transistors (TFTs) for next-generation displays. We have investigated the thermal distribution of an InSnZnO TFT under various gate and drain voltages by using an infrared imaging system. An asymmetrical thermal distribution was observed at a local drain region in a TFT depending on bias stress. These phenomena were decelerated or accelerated with stress time. We discussed the degradation mechanism by analyzing the electrical properties and thermal distribution. We concluded that the degradation phenomena are caused by a combination of Joule heating and the hot carrier effect.
Near unity ideality factor for sidewall Schottky contacts on un-intentionally doped β-Ga2O3 (2019)

We report a plasma damage removal method for β-Ga2O3 devices using hot phosphoric acid solution. Sidewall Schottky diodes were fabricated on MOCVD-grown un-intentionally doped β-Ga2O3 films grown on (010)-oriented semi-insulating substrates. Removal of the plasma damaged layers using wet etching resulted in near unity ideality factor and reduced hysteresis. The anisotropic etching behavior on the electrical characteristics of the devices was further evaluated, and the [001] direction was found to be a favorable direction for vertical device fabrications. The demonstrated damage removal method could enable a range of novel device architectures, including high power vertical diodes, vertical transistors and ultra-scaled devices.