gebhart/patrepeval huggingface dataset:
Physical mapping across the dihydrofolate reductase-thymidylate synthase chromosome of Leishmania major. (1997)

We have used a chromosome-specific approach to generate a 300 kb long 'contig' across Leishmania major 500 kb chromosome. Clones from a 13-hit genomic library served as templates to generate end-specific probes that were used in hybridization to a high density array of the library. The 'contig' generated contained 12 markers uniformly spaced. Three restriction endonucleases were mapped within the map extending its resolution. Map extension indicated a peculiar feature of sequence organization in subtelomeric regions where chromosome-specificity of mapping is lost. End-probes generated from clones mapping to the extremes of a 300 kb 'contig' rescued a high percentage of 2 types of clones from the genomic library, 1 of which showed positive hybridization to the hexameric telomere repeat. Fine mapping at these regions revealed that these 2 clones contained elements common to all chromosomes of the parasite. The physical map generated constitutes ready-to-use data for the study of many aspects of genome organization. Being cloned in a shuttle vector, the genomic sequences reordered in the map can be used to generate genetic information by transfection into the parasite.
The synthesis of di-carboxylate esters using continuous flow vortex fluidics (2015)

Faraday wave assisted flow chemistry. Vibrations and shear stress drive the synthesis of di-esters in minutes using room temperature vortex fluidics.
[Anti-foot-and-mouth vaccines combined with other bacterial or viral vaccines]. (1976)

Medical and sanitary prevention of a growing number of major infectious diseases of bovines has led IFFA-Mérieux to investigate the association of vaccines and to define methods of utilization. Care has been taken to limit the number of interventions and at the same time to retain in the combined valences the efficacy they had when in a state of single constituent. The work which has been carried out for the last ten years, including the study of adjuvants as well as of incompatibility of associations, has permitted the improvement of formulas, reduced in volume (5 ml for a plurivalent dose), in aqueous excipient (aluminum hydroxide and saponin) or oily excipient (oil in water type). These formulas combine 3 foot-and-mouth disease valences with a rabies valence (fixed strain grown on cell culture) or with a brucellosis valence (strain B. abortus MacEwen 45/20 and B. melitensis H 38). The innocuity of these associations allows them to be used in sanitary compaigns; their efficacy is equal to that of monovalent vaccines. A logical vaccination calendar is proposed.
CAWIS: Context aware wireless irrigation system (2014)

Water scarcity is one of the major problems faced by the whole world. In India, this situation is aggravated since agriculture is one of the major economies. As per the statistics of 2009, India has 35.12% of total land under irrigation. The objective of this work is to reduce the water usage in irrigation processes. In this regard, we have proposed a context aware wireless sensor network system for irrigation management. This multi-sensor system will continuously monitor the relevant environmental parameters, hydrological parameters, soil parameters and crop specific parameters to derive the context. These derived contexts will be used for automatic control and adaptation of the irrigation system. This context aware system uses the real-time sensor data to minimize the wastage of water used in the irrigation process. This research has also proposed an innovative design for horizontal angle adjustment of sprinkler nozzle using stepper motor. This remotely controllable sprinkler system can be wirelessly controlled, based on the decisions derived from the multi-sensors deployed in the agriculture field. The system also includes GSM module, which updates the user about the watering decisions being taken and executed on the fields. This paper describes the experimentation results of this system and it clearly shows that the system can effectively reduce water usage compared to the conventional systems.
SAT-292 Musashi: A Novel Regulator of the Gonadotrope Transcriptome (2020)

Abstract Sufficient nutrition is critical for reproduction. We have previously shown that leptin, a circulating indicator of fat stores, signals to pituitary gonadotropes to maintain gonadotropin releasing hormone receptor (GnRHR) protein levels in female mice. We hypothesized that this process is post-transcriptional, happening primarily through regulation of the RNA-binding protein Musashi (MSI). We showed that MSI binds to Gnrhr and inhibits translation, and a gonadotrope-specific deletion of Msi1 and Msi2 (Gon-Msi1/2-null) leads to increased GnRHR protein levels. This culminates in dysregulated luteinizing hormone (LH) and follicle-stimulating hormone (FSH). We have recently identified other gonadotrope and pituitary targets of MSI. We therefore suspected that MSI plays a role in both the maturation of gonadotropes and the normal cyclic regulation of gonadotropes. We hypothesized that the deletion of MSI would lead to downstream effects on (1) the composition of the gonadotrope population and (2) the molecular landscape of these cells. Using our adult, diestrous Gon-Msi1/2-null females, we performed single-cell RNA-sequencing on methanol-fixed dispersed pituitary cells. Libraries were made from two control pools and two mutant pools (n=3 pituitaries/pool) using 10x Genomics v3.1 Single-Cell Gene Expression technology and initially sequenced on an Illumina Next-seq mid-output flow-cell, yielding 5,000 reads/cell. Subsequent high-output sequencing obtained 25,000 reads/cell. We recovered single-cell mRNA transcript information from 18,206 control pituitary cells and 16,255 Gon-Msi1/2-null cells. Our analyses revealed that the Gon-Msi1/2-null pools had a higher % of cells expressing Fshb, as well as an expected significant drop in Msi2-expressing gonadotropes and no change in Lhb-expressing cells. We have recently identified Fshb as an MSI target in silico, and qRT-PCR of female pituitary lysate immunoprecipitated with anti-MSI1 shows a 7-fold enrichment in Fshb mRNA. We identified differentially expressed genes comparing the control and Gon-Msi1/2-null gonadotrope clusters. Using Gene Ontology analyses, the Gon-Msi1/2-null gonadotrope cluster appears to have aberrant expression of mRNAs involved in protein folding and cellular responses to nutrients. Our high-output sequencing has allowed us to achieve 25,000 reads/cell and will provide greater resolution of the role of Musashi in control of gonadotrope function. Taken together, our data indicate that Musashi influences the molecular landscape and subsequent physiology of the female gonadotrope. We have identified potential gonadotrope-specific MSI targets, including pathways that may underlie the dysregulated gonadotropin production and secretion seen in our Gon-Msi1/2-null females. Future studies will compare pubertal and adult females, as well as females from different estrous cycle stages.
Architectural support for dynamic reconfiguration of distributed workflow applications (1998)

In a distributed environment, it is inevitable that long running applications will require support for dynamic reconfiguration because, for example, machines may fail, services may be moved or withdrawn and user requirements may change. In such an environment it is essential that the structure of running applications can be modified to reflect such changes. A complication is that such long running applications are frequently composed out of existing applications. The resulting application can be very complex in structure, containing many temporal dependencies between constituent applications. This paper describes an approach that supports the dynamic reconfiguration of a class of large-scale distributed applications that represent business processes (commonly referred to as workflows). An application composition and execution environment has been designed and implemented as a transactional workflow system that enables sets of inter-related tasks (applications) to be carried out and supervised in a dependable manner. A task model that is expressive enough to represent temporal dependencies between constituent tasks has been developed. The workflow system maintains this structure and makes it available through transactional operations for performing changes to it. Use of transactions ensures that changes can be carried out atomically with respect to running applications. The workflow system is general purpose and open: it has been designed and implemented as a set of CORBA services to run on top of a given ORB.
Bordetella pertussis adenylate cyclase: isolation and purification by calmodulin-sepharose 4B chromatography (1987)

Purified preparations of adenylate cyclase were obtained from crude urea extracts of Bordetella pertussis by a one-step calmodulin affinity chromatography technique. Diluted extract was loaded onto the column and washed, and adenylate cyclase was eluted with 10mM EGTA [ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid]. A 104-fold purification was accomplished in one step. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the affinity-purified adenylate cyclase was dissociated into one major protein band with an apparent molecular weight of 60,000 and a minor band at 200,000. The affinity-purified adenylate cyclase was observed to have adenylate cyclase enzymatic activity which was activated by calmodulin, to bind 125I-calmodulin, and to be free of pertussis toxin as determined by in vivo and in vitro assays.
High Resolution Magic Angle Spinning Proton NMR Study of Alzheimer’s Disease with Mouse Models (2022)

Alzheimer's disease (AD) is a crippling condition that affects millions of elderly adults each year, yet there remains a serious need for improved methods of diagnosis. Metabolomic analysis has been proposed as a potential methodology to better investigate and understand the progression of this disease; however, studies of human brain tissue metabolomics are challenging, due to sample limitations and ethical considerations. Comprehensive comparisons of imaging measurements in animal models to identify similarities and differences between aging- and AD-associated metabolic changes should thus be tested and validated for future human non-invasive studies. In this paper, we present the results of our highresolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) studies of AD and wild-type (WT) mouse models, based on animal age, brain regions, including cortex vs. hippocampus, and disease status. Our findings suggest the ability of HRMAS NMR to differentiate between AD and WT mice using brain metabolomics, which potentially can be implemented in in vivo evaluations.
Visible Versus Near-Infrared Optical Performance of Diffractive Multifocal Intraocular Lenses (2015)

In addition to changes in add power, the optical performances of the DMIOLs measured under either VIS or NIR illumination are considerably different. Whereas they show two distinct (near and far) foci under VIS light, their optical performances under NIR illumination are clearly biased in favor of their far focus. These results may help prevent a misleading use of NIR-based clinical instruments for the assessment of eyes implanted with DMIOLs.
Thermal Properties of Silica Aerogel Formula (2015)

The thermal conductivity of silica aerogel developed in this research program was measured using the transient hot-wire technique. The thermal conductivity of monolithic samples drops significantly from 9.3 mW/m · K to 3.2 mW/m · K with modest pressure reduction from 1 atm to 0.1 atm. The same aerogel in granular form has a thermal conductivity of 15.0 mW/m · K at ambient gas pressure with a modest compression applied to compact the granules and reduce the air void sizes. Radiation heat transfer in the hot-wire test may not be representative of its contribution in large scale applications. Measurements of the monochromatic extinction coefficient over the wavelengths of interest resulted in a Rosseland mean extinction coefficient of 2400 m[superscript −1] at 300 K. The small thermal penetration distance during the hot-wire measurements suggest that in actual use radiation could contribute approximately 2.5 mW/m · K with a possible upper limit of 3.0 mW/m · K to the effective thermal conductivity over that measured using the transient hot-wire method.
Activation of MET signaling by HDAC6 offers a rationale for a novel ricolinostat and crizotinib combinatorial therapeutic strategy in diffuse large B‐cell lymphoma (2018)

Some histone deacetylases (HDACs) promote tumor cell growth and pan- or selective HDAC inhibitors are active in some cancers; however, the pivotal HDAC enzyme and its functions in human diffuse large B-cell lymphoma (DLBCL) remain largely unknown. Using NanoString nCounter assays, we profiled HDAC mRNA expression and identified HDAC6 as an upregulated HDAC family member in DLBCL tissue samples. We then found that HDAC6 plays an oncogenic role in DLBCL, as evidenced by its promotion of cell proliferation in vitro and tumor xenograft growth in vivo. Mechanistically, the interaction between HDAC6 and HR23B downregulated HR23B expression, thereby reducing the levels of casitas B-lineage lymphoma (c-Cbl), an E3 ubiquitin ligase for hepatocyte growth factor receptor (MET), which resulted in the inhibition of MET ubiquitination-dependent degradation. In addition, enhanced HDAC6 expression and decreased HR23B expression were correlated with poor overall survival rates among patients with DLBCL. Taken together, these results establish an HDAC6-HR23B-MET axis and indicate that HDAC6 is a potent promoter of lymphomagenesis in DLBCL. Thus, a therapeutic strategy based on HDAC6 inhibitors in combination with MET inhibitors is promising. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Escaping Printable Encoded Streams to Embed Out-of-Band Data (2023)

In this paper, we propose to exploit the unused configurations of a printable encoding such as Base41, Base45 or Base85 to create a side channel that can store extra data such as error detection or correction codes, integrity verification and authentication information or application defined data. After introducing the encoding of binary octet strings in printable form, we present some case studies that show possible applications of the unused configurations.
Late-onset facial abscess formation after cosmetic soft tissue augmentation with bio-alcamid (2007)

Bio-Alcamid (BA) (polyalkylimide) was introduced in Europe in 2001. It is a nonresorbable injectable filler for soft tissue augmentation, indicated for a wide variety of clinical applications in reconstructive and cosmetic surgery in conditions where subcutaneous volumetric compensation is required. Although BA biocompatibility was approved by a European Union Certificate (CE), the substance is not a natural component of biologic tissues, and thus inflammation and infection are still potential risks. The authors present a case of BA infection after minor trauma 3 years after bilateral injections to the malar regions in a 43-year-old woman, causing an abscess that required surgical drainage and parenteral antibiotics.
A review of regulatory standard test methods for residential wood heaters and recommendations for their advancement (2023)

In many regions, residential wood heaters are a leading source of harmful air pollution but only satisfy a small portion of local heating demands. In response, standardized laboratory test methods have been developed to characterize and limit wood heater emissions. While these test methods are a key tool for advancing both wood heater technology and environmental regulations, many of the experimental procedures are outdated and provide few actionable insights for improving heater performance. Furthermore, these test methods vary widely around the world and may not adequately capture the performance of wood heaters operating in residences. This study presents a comprehensive review of standardized wood heater test methods to identify fundamental experimental objectives and regulated performance metrics. Using the results of this review, recommendations are provided to make the test methods more accessible and representative of residential performance, while generating actionable data to motivate heater design improvements. This study elucidates the current state of standard test methods, and the developments needed to advance clean wood heater technologies and public policies.
Aurora A activation in mitosis promoted by BuGZ (2017)

Protein phase separation or coacervation has emerged as a potential mechanism to regulate biological functions. We have shown that coacervation of a mostly unstructured protein, BuGZ, promotes assembly of spindle and its matrix. BuGZ in the spindle matrix binds and concentrates tubulin to promote microtubule (MT) assembly. It remains unclear, however, whether BuGZ could regulate additional proteins to promote spindle assembly. In this study, we report that BuGZ promotes Aurora A (AurA) activation in vitro. Depletion of BuGZ in cells reduces the amount of phosphorylated AurA on spindle MTs. BuGZ also enhances MCAK phosphorylation. The two zinc fingers in BuGZ directly bind to the kinase domain of AurA, which allows AurA to incorporate into the coacervates formed by BuGZ in vitro. Importantly, mutant BuGZ that disrupts the coacervation activity in vitro fails to promote AurA phosphorylation in <i>Xenopus laevis</i> egg extracts. These results suggest that BuGZ coacervation promotes AurA activation in mitosis.
Singular Value Decomposition and Principal Component Analysis (2005)

This chapter describes gene expression analysis by Singular Value Decomposition (SVD), emphasizing initial characterization of the data. We describe SVD methods for visualization of gene expression data, representation of the data using a smaller number of variables, and detection of patterns in noisy gene expression data. In addition, we describe the precise relation between SVD analysis and Principal Component Analysis (PCA) when PCA is calculated using the covariance matrix, enabling our descriptions to apply equally well to either method. Our aim is to provide definitions, interpretations, examples, and references that will serve as resources for understanding and extending the application of SVD and PCA to gene expression analysis.
Nematic Anisotropic Liquid‐Crystal Gels—Self‐Assembled Nanocomposites with High Electromechanical Response (2003)

Abstract The uniqueness of liquid crystals (LCs) lies in the large anisotropies of their properties, which can be utilized to generate high electromechanical responses. In a properly oriented LC polymer system, an external electric field can induce reorientation of the mesogenic units possessing a dielectric anisotropy, which, when coupled with the shape anisotropy of the mesogenic units, can in turn produce large mechanical strain. Anisotropic LC gels, which can be obtained by in‐situ photopolymerization of the reactive LC molecules in the presence of non‐reactive LC molecules in an oriented state, are an example of such liquid‐crystal polymer systems. It is shown here that a homeotropically aligned LC gel in its nematic phase exhibits high electrically induced strain (&gt; 2 %) with an elastic modulus of 100 MPa and a high electromechanical conversion efficiency (75 %) under an electric field of 25 MV/m. These anisotropic LC polymeric materials could provide a technologically compatible system for such applications as artificial muscles and as microelectromechanical devices.
Cation Binding to Halorhodopsin (2015)

A member of the retinal protein family, halorhodopsin, acts as an inward light-driven Cl(-) pump. It was recently demonstrated that the Natronomonas pharaonis halorhodopsin-overproducing mutant strain KM-1 contains, in addition to the retinal chromophore, a lipid soluble chromophore, bacterioruberin, which binds to crevices between adjacent protein subunits. It is established that halorhodopsin has several chloride binding sites, with binding site I, located in the retinal protonated Schiff base vicinity, affecting retinal absorption. However, it remained unclear whether cations also bind to this protein. Our electron paramagnetic resonance spectroscopy examination of cation binding to the halorhodopsin mutant KM-1 reveals that divalent cations like Mn(2+) and Ca(2+) bind to the protein. Halorhodopsin has a high affinity for Mn(2+) ions, which bind initially to several strong binding sites and then to binding sites that exhibit positive cooperativity. The binding behavior is pH-dependent, and its strength is influenced by the nature of counterions. Furthermore, the binding strength of Mn(2+) ions decreases upon removal of the retinal chromophore from the protein or following bacterioruberin oxidation. Our results also indicate that Mn(2+) ions, as well as Cl(-) ions, first occupy binding sites other than site I. The observed synergetic effect between cation and anion binding suggests that while Cl(-) anions bind to halorhodopsin at low concentrations, the occupancy of site I requires a high concentration.
Energy-Efficient Dual-Iteration Power Allocation for Two-Phase Relay System with Massive Antennas (2014)

This paper considers the scenario where multiple source nodes communicate with multiple destination nodes simultaneously with the aid of an amplify-and-forward relay equipped with massive antennas. In order to achieve optimal energy efficiency (EE) of the entire relay system, this paper investigates the power allocation problem for the multiple pairs of nodes at both the source nodes and the relay node, where the relay employs the backward and forward zero-forcing filters. Since the EE optimization problem cannot be solved analytically, we propose a two-phase power allocation method. Given power allocation of one phase, the optimal power allocation is derived for the other phase. Furthermore, two dual-iteration power allocation (DIPA) algorithms with performance approaching that of optimal EE are developed based on the instantaneous and statistic channel state information, respectively. Numerical results show that the proposed DIPA algorithms can greatly improve EE while guaranteeing spectrum efficiency (SE) when compared with the equal power allocation algorithm. Moreover, both algorithms suggest that deploying a rational number of antennas at the relay node and multiplexing a reasonable number of node pairs can improve on the EE and SE.
ADAPTIVE VOXEL SUBDIVISION FOR RAY TRACING (1988)

Although regular subdivision has been shown to be efficient at ray tracing scenes where objects are evenly distributed, such algorithms perform poorly when objects are concentrated in a small number of voxels. In this paper, a method is presented where voxels in a regular grid are examined and recursively subdivided depending on object density. This integration of regular and adaptive spatial subdivision methods allows images consisting of large regularly distributed objects and small dense objects to be ray traced efficiently. The parameters controlling the coarseness of the voxel grid, depth of adaptive subdivision trees, and maximum number of polygons per voxel are varied and their effects on execution time, subdivision time, and memory use are measured.