gebhart/patrepeval huggingface dataset:
A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis (2009)

The extraordinary mt genome of R. similis with its unique genetic code appears to contain exceptional features correlated to DNA decoding. Therefore the genome may provide an incentive to further elucidate these barely understood processes in nematodes. This comprehension may eventually lead to parasitic nematode-specific control targets as healthy mitochondria are imperative for organism survival. In addition, the presented genome is an interesting exceptional event in genetic code evolution.
Towards a national infectious disease information infrastructure: a case study in West Nile virus and botulism (2004)

Information technologies are playing an increasingly important role in preventing, detecting, and managing infectious disease outbreaks. This paper presents a collaborative infectious disease informatics project led by an interdisciplinary team of information systems researchers and public health researchers and practitioners. This project has resulted in a research prototype called the WNV-BOT Portal system, which provides an integrated infectious disease information sharing, analysis, and visualization environment across jurisdictions.
In Situ Hybridization: An Informative Technique for Pigment Cell Researchers (2004)

Many cellular events are regulated at the transcriptional level. Recent technical advances such as DNA microarray have made it possible to determine mRNA profiles of cultured cells or tissues. However, since it is still impossible to completely simulate the in vivo environment in culture conditions, mRNA profiles of cultured cells are not perfect representatives of original cells. Furthermore, for cells that exist at lower densities, mRNA profiling using tissue samples would be difficult. By using tissue in situ hybridization, mRNA levels of genes in tissues can be determined at cellular resolution. Although throughput of tissue in situ hybridization is not high enough for mRNA profiling, it may be sufficient to investigate temporal/spatial expression profiles of genes that are known to be important or found to be interesting in high-throughput transcriptome/proteome analyses. Recent technical advances have made it easier for everybody to perform tissue in situ hybridization using normal experimental instruments with sufficient sensitivity to detect most genes. Although this technique has been utilized mainly in developmental biology, it will be fully advantageous when combined with high-throughput comprehensive transcriptome/proteome analyses.
The phase angle in second harmonic alternating current polarography (1964)

Abstract Second harmonic polarograms in which, as predicted by theory, every reversible redox system gives rise to two peaks have been described in the literature 1, 2, 3 . In this paper the π radians phase difference between these two peaks is demonstrated, making use of the second harmonic content of the output of the oscillator driving the polarographic circuit. Anomalies in the case of the Tl(Hg)/Tl ⊕ ‐ and the In(Hg)/In ⊕⊕⊕ ‐electrode are discussed.
Solar Desalination With Latent Heat Recovery (1988)

Unlike conventional solar stills, the present system utilizes the latent heat of condensation and the sensible heat of the discarded seawater. The performance was optimized analytically and the system is presently under construction in Egypt. The system consists of a humidifier, a solar still or channel, a condenser, and a pond. In the humidifier, ambient air is humidified and heated by a warm brine from the pond. If the brine outlet temperature is higher than the ambient temperature, it goes back to the pond, if not, it is discarded. The solar still is a long glass-covered channel, about 200 meters long.
Comparison of sulfoquinovosyl diacylglycerol from spinach and the purple bacteriumRhodobacter sphaeroides by fast atom bombardment tandem mass spectrometry (1992)

Isolated sulfoquinovosyl-diacylglycerol (SQD) from spinach and the purple bacterium Rhodobacter sphaeroides provide two sources of very different molecular species of SQD. We were able to demonstrate by fast atom bombardment-collisionally activated dissociation tandem mass spectrometry in the negative ion mode that the sulfoquinovosyl head group of the plant and bacterial lipids can be characterized by the common fragmentation pattern found in the spectra of both samples. Differences in the acyl functions from the two sources were also identified by this technique. SQD specific fragments are found at m/z 299, 283, 241, 225, 165 and 80 which indicate the presence of the sulfoquinovosyl moiety. The two predominant molecular species found in spinach contain palmitic and linolenic ([M-H]- at m/z 815) or two linolenic acids ([M-H]- at m/z 837) in the sn-1 and sn-2 positions, while the two major species of the bacterial lipid contain palmitic and 18:1 (vaccenic) acids ([M-H]- at m/z 819) or stearic and 18:1 (vaccenic) acids, ([M-H]- at m/z 847), respectively.
Motion planning for long reach manipulation in aerial robotic systems with two arms (2017)

In this paper an aerial robotic system with two arms for long reach manipulation (ARS-LRM) while flying is presented. The system consists of a multirotor with a long bar extension that incorporates a lightweight dual arm in the tip. This configuration allows aerial manipulation tasks increasing considerably the safety distance between rotors and manipulated objects. The objective of this work is the development of planning strategies to move the ARS-LRM system for both navigation and manipulation tasks. With this purpose, a simulation environment to evaluate the algorithms under consideration is required. Consequently, the ARS-LRM dynamics has been properly modeled with specific methodologies for multi-body systems. Then, a distributed control scheme that makes use of nonlinear control strategies based on model inversion has been derived to complete the testbed. The motion planning problem is addressed considering jointly the aerial platform and the dual arm in order to achieve wider and safer operating conditions. The operation of the planner is given by an RRT*-based algorithm that optimizes energy and time performance in cluttered environments for both navigation and manipulation tasks. This motion planning strategy has been tested in a realistic industrial scenario given by a riveting task. The satisfactory results of the simulations are presented as a first validation of the proposed approach.
Soil Loss Minimization through Land Use Optimization (2012)

The optimal allocation of the limited land resources in a watershed scale is one of the most important factors of reducing the volume of soil erosion. Applying optimization techniques can empower the decision-maker or watershed manager to maintain a reasonable balance between environmental flows and demands. The main objective of this research is to study the optimized combination of land allocation to different land uses like forestland, rangeland, orchard, irrigated farming and dry farming for minimized soil erosion in Abolabbas watershed located in Khuzestan province, Iran. For this purpose an optimization problem based on linear programming solution has been formulated in three different land use scenarios including existing land uses, existing land uses and some land management and finally optimum land uses with proper land management. Using simplex method within the LINGO software, the optimal solution was determined. The results demonstrated that the amount of soil erosion could, respectively reduce to the tune of 1.70, 69.77 and 75.85%, in three scenarios, in case of implementing optimal allocation of land resources in different land uses. The results of sensitivity analysis also showed that the area of orchard and irrigated lands are the most sensitive parameters in the constraints of soil erosion minimization problem.
A Corrosion Sensor for Integrated State-of-Health Evaluation. (2016)

Abstract not provided.
Practical Guide to Optical Alignment (2017)

Lasers are often used for the alignment of optical systems, because they remain parallel over large distances. They can specifically be introduced into a setup for alignment needs or are sometimes already present for other purposes. Such a laser usually defines the optical axis, which should traverse the precise center of all lenses and other optical elements.
Abstract PR5: Identifying mechanisms of drug resistance to MAPK pathway inhibition via genome-scale rescue screens (2012)

Abstract The recent clinical success of RAF inhibitors in BRAF(V600E)-mutant malignant melanoma highlights the promise of targeted therapeutics as well as the inevitability of acquired drug resistance: responses are sustained for less than a year and all patients ultimately become drug resistant. To identify causative drug resistance genes in BRAF(V600E)-mutant melanoma, we have individually expressed over 14, 000 unique genes and queried their ability to affect sensitivity to a panel of mitogen activated protein kinase (MAPK) pathway inhibitors, including a RAF, MEK and ERK inhibitor, both as single agents or in combination (RAFi+MEKi). Out of this genome-scale collection, less than 1% of genes are sufficient to induce resistance to the MAPK pathway inhibitors tested. Here, we present the results of this rescue screen and extensive validation/characterization efforts that reveal a number of novel insights into mechanisms of drug resistance, melanoma biology and the MAPK signaling pathway. Additionally, the scale of this first-of-kind functional rescue screen permits its integration with existing genome characterization efforts, including melanoma sequencing studies, gene expression data and parallel functional assays to identify the most relevant genetic modifiers of resistance to MAPK pathway inhibition. This proffered talk is also presented as Poster B27.
GSK3β modulates NF-κB activation and RelB degradation through site-specific phosphorylation of BCL10 (2018)

Glycogen synthase kinase 3β (GSK3β) is a ubiquitously expressed serine/threonine kinase involved in the regulation of various cellular functions, such as energy homoeostasis, cell growth and developmental processes. More recently, GSK3β has been identified as a part of a protein complex involved in the regulation of the CARMA1-BCL10-MALT1 complex (CBM complex) formation, which is a key signalling event upon antigen receptor engagement of B and T cells, required for the activation of the NF-κB and JNK pathways. However, conflicting reports have been published regarding the role of GSK3β for the activation of the NF-κB signalling pathways. Therefore, we aimed to determine the impact of GSK3β on the NF-κB signalling induced upon T cell activation. Blocking GSK3β by either pharmacologic inhibitors (SB216763 and SB415286) or by RNAi caused a reduced proteolysis of the MALT1 targets CYLD1, BCL10 and RelB as well as diminished IκBα degradation, NF-κB DNA binding and NF-κB activity. This negative effect on NF-κB appears to be due to a diminished CBM complex formation caused by a reduced BCL10 phosphorylation. Taken together, we provide here evidence for a novel regulatory mechanism by which GSK3β affects NF-κB signalling in activated T cells.
Clinical evaluation of synthetic computed tomography methods in adaptive proton therapy of lung cancer patients (2023)

Both sCT methods were judged to be of clinical quality and valuable for reducing the amount of reCT acquisitions.
Determination of optical parameters of human breast tissue from spatially resolved fluorescence: a diffusion theory model (2002)

We report the measurement of optical transport parameters of pathologically characterized malignant tissues, normal tissues, and different types of benign tumors of the human breast in the visible wavelength region. A spatially resolved steady-state diffuse fluorescence reflectance technique was used to estimate the values for the reduced-scattering coefficient (mu(s)') and the absorption coefficient (mu(a)) of human breast tissues at three wavelengths (530, 550, and 590 nm). Different breast tissues could be well differentiated from one another, and different benign tumors could also be distinguished by their measured transport parameters. A diffusion theory model was developed to describe fluorescence light energy distribution, especially its spatial variation in a turbid and multiply scattering medium such as human tissue. The validity of the model was checked with a Monte Carlo simulation and also with different tissue phantoms prepared with polystyrene microspheres as scatterers, riboflavin as fluorophores, and methylene blue as absorbers.
Composição química das 9-11AS costelas de tourinhos Nelore e cruzados terminados em confinamento em relação ao status nutricional na fase de pastejo. (2006)

Duzentos e trinta e seis tourinhos Nelore (NE) e cruzados Y2 Canchim + Y2 Nelore (CN), Y2 Angus + Y2 Nelore (AN) e Y2 Simental + Y2 Nelore (SN), recriados com dois níveis de ingestão de concentrado (O e 3 kg/animal.dia), em pastagem de coast-cross adubada, foram confinados e receberam silagem de milho (60%) e concentrado (40%). Os animais da linha base foram abatidos com peso médio de 329 kg e média de composição química da seção 9-11 a costelas de 64,3% de água, 19,0% de proteína bruta, 12,3% extrato etéreo e 4,4% matéria mineral. A suplementação durante a recria proporcionou maior teor de extrato etéreo no corte das costelas dos animais que entraram no confinamento. Após o confinamento o peso médio de abate foi de 487kg e a composição da 9-11 a costelas foi 57,3%, 16,9%, 21,3% e 4,5% de água, proteína bruta, extrato etéreo e matéria mineral respectivamente. Não houve interação entre grupo genético e nível de suplementação. Os animais Nelore ap resentaram maior teor de extrato etéreo e menor teor de água (P&lt;0,05) e que os cruzados, sendo que os animais cruzados Simental x Nelore apresentaram maior teor de proteína bruta e menor de extrato etéreo que os demais genótipos. PALAVRAS-CHAVE Angus, Canchim, composição corporal, Nelore, Simental
Carbon monoxide protects against hemorrhage and resuscitation-induced endothelial/microcirculatory injury (2013)

Nassour, Ibrahim MD; Carchman, Evie H. MD; Kautza, Benjamin MD; Whelan, Sean P. MD; Escobar, Daniel MD; Otterbein, Leo E. PhD; Zuckerbraun, Brian S. MD, FACS Author Information
Membrane separation process for soybean oil refining and its economical effects. (1986)

A feasibility has been studied, on physical process for refining soybean oil by using ultra-filtration.In this work, the following was clarified. The solvent-resistant polyimide ultrafiltration membrane, which is available from Nitto Electric Industrial Co., Ltd., designated as NTU-4200, is effective for processing soybean miscella at 40°C, and molecular weight cutoff Value 20000 of the polyimide ultrafiltration membrane gives good results for degumming soybean miscella. And, total physical refining process of soybean oil is practicable.From economical estimation by bench-scale test plant, physical refining of soybean oil by use of membrane separation is effectively profitable, comparing with the conventional chemical refining. This might be epochmaking matter for oil industry.
Audio restoration by constrained audio texture synthesis (2004)

Audio texture, a new audio medium, is used to synthesize long audio streams according to a given short example audio clip. In this paper, we extend this idea to audio texture restoration, or constrained audio texture synthesis for restoring those missing parts in an audio clip. It is useful in many applications such as audio restoration and audio reconstruction. It can also be used in error concealment for audio/music delivery with packet loss on the Internet. A novel method is proposed for constrained audio texture synthesis. Preliminary results are provided for evaluation.
ISE01-1: An Overlay Server System (OSS) Platform for Multiplayer Online Games over Mobile Networks (2006)

We propose a gaining architecture, called the overlay server system (OSS), for supporting multiparty online games over mobile networks. In OSS architecture, overlay server nodes (OSN) are distributed across the core network architecture of the mobile operator and each node is responsible for both running the game applications and performing the overlay routing. The architecture allows third party game servers that are located outside the core network of the mobile operator to push the execution of delay and bandwidth constrained game components into the core to achieve better quality of service (QoS). When a game consists of multiple mutually exclusive game objects such that each object can be maintained independently, OSS allows per object QoS optimization via selecting the jointly optimal location (i.e. OSN) and overlay routes for each object. This fine-grain optimization benefits most when different objects have different QoS requirements and they are accessed by different users. OSS dynamically adapts to the changes in game and network conditions by switching to better OSN and overlay routes. Our performance analysis on different core network topologies and usage patterns demonstrates that OSS has significant advantages over the alternative peer to peer (P2P), proxy-server, and client-server architectures. The analysis also underlines the individual contributions of object placement and jointly performed overlay route optimization to the performance gain.
Explosive joining for the Mars Sample Return Mission (2000)

A unique, small-scale, ribbon explosive joining process is being developed as an option for closing and sealing a metal canister to allow the return of a pristine sample of the Martian surface and atmosphere to Earth. This joining process is accomplished by an explosively driven, high-velocity, angular collision of the metal, which melts and effaces the oxide films from the surfaces to allow valence electron sharing to bond the interface. Significant progress has been made through more than 100 experimental tests to meet the goals of this ongoing developmental effort. The metal of choice, aluminum alloy 6061, has been joined in multiple interface configurations and in complete cylinders. This process can accommodate dust and debris on the surfaces to be joined. It can both create and sever a joint at its midpoint with one explosive input. Finally, an approach has been demonstrated that can capture the back blast from the explosive.
Supplementary Table S1 from Multivalent Peptoid Conjugates Which Overcome Enzalutamide Resistance in Prostate Cancer Cells (2023)

&lt;p&gt;IC50 of enzalutamide and MPC6 in prostate cancer cell lines.&lt;/p&gt;
Alterations of intralesional and lymph node gene expression and cellular composition induced by IL‐12 administration during leishmaniasis (2001)

Changes in gene expression and cellular distribution in the lymph node and at the site of infection, the footpad, during Leishmania major infection and/or IL-12 administration were evaluated. Otherwise susceptible BALB/c mice given IL-12 are able to resolve infection. Interestingly, iNOS was not induced in the lymph node by IL-12, yet, nitric oxide is critical in the control of leishmaniasis. However, we observed an increase in iNOS at the lesion site in response to IL-12. These results reflect the importance of examining the primary site of infection. We observed no changes in inflammation at the lesion site; however, IL-12 promoted an early inflammatory response in the lymph nodes. IL-12 administration differentially affected both the local and systemic immune response to invading leishmanial parasites. IL-12 induced iNOS at the lesion site and an early granulomatous inflammation in the lymph node; therefore, we hypothesize that these are key events responsible for the resolution of disease in BALB/c mice treated with IL-12.
A double-blind study of food extract injection therapy: a preliminary report. (1977)

A double-blind, crossover study of food extract injection therapy is reported. There was a significantly better response to food injection therapy than to placebo. In many cases the response of lifelong, severe, intractable syndromes was rapid and dramatic, often beginning in three to four days, and symptoms often returned within three to four days after beginning a course of placebo therapy. In clinical practice this should prove to be a useful practical tool for demonstrating the etiologic role of foods and providing substantial relief in several serious syndromes for which no other satisfactory method of etiologic diagnosis or effective therapy is available.
Noise-robust classification of single-shot electron spin readouts using a deep neural network (2021)

Abstract Single-shot readout of charge and spin states by charge sensors such as quantum point contacts and quantum dots are essential technologies for the operation of semiconductor spin qubits. The fidelity of the single-shot readout depends both on experimental conditions such as signal-to-noise ratio, system temperature, and numerical parameters such as threshold values. Accurate charge sensing schemes that are robust under noisy environments are indispensable for developing a scalable fault-tolerant quantum computation architecture. In this study, we present a novel single-shot readout classification method that is robust to noises using a deep neural network (DNN). Importantly, the DNN classifier is automatically configured for spin-up and spin-down traces in any noise environment by tuning the trainable parameters using the datasets of charge transition signals experimentally obtained at a charging line. Moreover, we verify that our DNN classification is robust under noisy environment in comparison to the two conventional classification methods used for charge and spin state measurements in various quantum dot experiments.
Psychedelic resting-state neuroimaging: a review and perspective on balancing replication and novel analyses (2021)

Clinical research into serotonergic psychedelic drugs including psilocybin, LSD and N,N-DMT (e.g., in ‘ayahuasca’) is expanding rapidly and clinical trials across a range of psychiatric conditions have shown promising efficacy, with larger trials ongoing. Resting-state functional magnetic resonance imaging (fMRI) has emerged as a brain imaging strategy commonly used to identify associated neural mechanisms in both clinical and healthy populations. To date, 42 research articles have been published analysing resting-state fMRI data from 17 unique datasets involving the administration of a psychedelic drug. This provides a promising foundation for resolving imaging markers of the perceptual and clinical effects of psychedelics. Here we review the existing psychedelic resting-state fMRI literature through a lens that brings attention to emerging variation in core methodological decisions and promote strategies that aim to strengthen the field. We find a large degree of heterogeneity across the existing literature, with nearly all studies varying in data processing and analysis or drug evaluated. Two datasets are the foundation of more than half of the published literature, and terms such as “entropy” are often used to denote distinct metrics across studies. In light of these observations, we offer suggestions for future studies that we hope encourages coherence in the field. As a budding field of interest, psychedelic resting-state imaging will benefit from the development of novel models, hypotheses and quantification methods that may expand our understanding of the neural mechanisms mediating the intriguing acute perceptual and lasting clinical effects. Our review of the existing literature suggests that the psychedelic resting-state brain imaging field is at a crossroads at which it must also consider the critical importance of consistency and replicability to effectively converge on stable representations of the neural effects of psychedelics.
A Cell-based Heuristics for Guide Path Layout Design for AGV Systems (2018)

In this paper, we consider the guide path layout design problem considering guide path design costs and flow travel costs for automated guided vehicle (AGV) systems. A cell-based heuristics is proposed. The performances of model and heuristics are compared in the computational experiments.