gebhart/patrepeval huggingface dataset:
Significance of Aberrant Expression of MicroRNAs in Cancer Cells (2008)

Alterations in miRNA genes and other non-coding RNAs play a critical role in the pathophysiology of all human cancers: cancer initiation and progression can involve microRNAs (miRNAs) – small non-coding RNAs that can regulate gene expression. At present, the main mechanism of microRNoma (defined as the full complement of microRNAs present in a genome) alteration in cancer cells seems to be represented by aberrant gene expression, characterized by abnormal levels of expression for mature and/or precursor miRNA sequences in comparison with the corresponding normal tissues. MicroRNAs expression profiling has been exploited to identify miRNAs that are potentially involved in the pathogenesis of human cancers. MicroRNAs and other non-coding RNAs profiling achieved by various methods has allowed the identification of signatures associated with diagnosis, staging, progression, prognosis, and response to treatment of human tumors.
Assigning amino acid sequences to 3‐dimensional protein folds (1996)

With the advent of genome sequencing projects, the amino acid sequences of thousands of proteins are determined every year. Each of these protein sequences must be identified with its function and its 3-dimensional structure for us to gain a full understanding of the molecular biology of organisms. To meet this challenge, new methods are being developed for fold recognition, the computational assignment of newly determined amino acid sequences to 3-dimensional protein structures. These methods start with a library of known 3-dimensional target protein structures. The new probe sequence is then aligned to each target protein structure in the library and the compatibility of the sequence for that structure is scored. If a target structure is found to have a significantly high compatibility score, it is assumed that the probe sequence folds in much the same way as the target structure. The fundamental assumptions of this approach are that many different sequences fold in similar ways and there is a relatively high probability that a new sequence possesses a previously observed fold. We review various approaches to fold recognition and break down the process into its main steps: creation of a library of target folds; representation of the folds; alignment of the probe sequence to a target fold using a sequence-to-structure compatibility scoring function; and assessment of significance of compatibility. We emphasize that even though this new field of fold recognition has made rapid progress, technical problems remain to be solved in most of the steps. Standard benchmarks may help identify the problem steps and find solutions to the problems.
GraphVista: Interactive Exploration Of Large Graphs (2015)

The potential to gain business insights from graph-structured data through graph analytics is increasingly attracting companies from a variety of industries, ranging from web companies to traditional enterprise businesses. To analyze a graph, a user often executes isolated graph queries using a dedicated interface---a procedural graph programming interface or a declarative graph query language. The results are then returned and displayed using a specific visualization technique. This follows the classical ad-hoc Query$\rightarrow$Result interaction paradigm and often requires multiple query iterations until an interesting aspect in the graph data is identified. This is caused on the one hand by the schema flexibility of graph data and on the other hand by the intricacies of declarative graph query languages. To lower the burden for the user to explore an unknown graph without prior knowledge of a graph query language, visual graph exploration provides an effective and intuitive query interface to navigate through the graph interactively. We demonstrate GRAPHVISTA, a graph visualization and exploration tool that can seamlessly combine ad-hoc querying and interactive graph exploration within the same query session. In our demonstration, conference attendees will see GRAPHVISTA running against a large real-world graph data set. They will start by identifying entry points of interest with the help of ad-hoc queries and will then discover the graph interactively through visual graph exploration.
Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target (2012)

Malarial dihydrofolate reductase (DHFR) is the target of antifolate antimalarial drugs such as pyrimethamine and cycloguanil, the clinical efficacy of which have been compromised by resistance arising through mutations at various sites on the enzyme. Here, we describe the use of cocrystal structures with inhibitors and substrates, along with efficacy and pharmacokinetic profiling for the design, characterization, and preclinical development of a selective, highly efficacious, and orally available antimalarial drug candidate that potently inhibits both wild-type and clinically relevant mutated forms of Plasmodium falciparum (Pf) DHFR. Important structural characteristics of P218 include pyrimidine side-chain flexibility and a carboxylate group that makes charge-mediated hydrogen bonds with conserved Arg122 (PfDHFR-TS amino acid numbering). An analogous interaction of P218 with human DHFR is disfavored because of three species-dependent amino acid substitutions in the vicinity of the conserved Arg. Thus, P218 binds to the active site of PfDHFR in a substantially different fashion from the human enzyme, which is the basis for its high selectivity. Unlike pyrimethamine, P218 binds both wild-type and mutant PfDHFR in a slow-on/slow-off tight-binding mode, which prolongs the target residence time. P218, when bound to PfDHFR-TS, resides almost entirely within the envelope mapped out by the dihydrofolate substrate, which may make it less susceptible to resistance mutations. The high in vivo efficacy in a SCID mouse model of P. falciparum malaria, good oral bioavailability, favorable enzyme selectivity, and good safety characteristics of P218 make it a potential candidate for further development.
Trend-MC: A Melody Composer by Constructing from Frequent Trend-Based Patterns (2015)

Algorithmic composition refers to the process of composing a melody automatically using algorithms. A bulk of methods have been proposed for this task. Among them, a novel idea is to utilize the correlation information between the pitches of melodies and the tones of lyrics for melody composition. Unfortunately, the existing method adopting this idea suffers from several severe shortcomings and thus the merits of the above idea are not fully utilized. In this paper, we propose a new technique to capture the above correlation information based on the concepts of pitch trends and tone trends. Based on this technique, we design a new algorithm called Trend-MC for melody composition which avoids the shortcomings of the existing method. We also developed a software with the Trend-MC algorithm as its core. We demonstrate that the software could compose nice melodies with the input of lyrics.
Quantum cascade laser: a unipolar intersubband semiconductor laser operating at 125 K (2005)

A new semiconductor injection laser (Quantum Cascade Laser) which differs in a fundamental way fiom diode lasers has been demonstrated. It relies on only one type of carrier (it is a unipolar semiconductor laser), and on electronic transitions between conduction band energy levels of quantum wells. Such intersubband lasers were originally proposed 25 years ago, but despite considerable effort thip ;s the first structure to achieve laser action. The present device operates at a wavelength of 4.26 microns, but since the wavelength is entirely determined by quantum confinement, it can be tailored from the mid-infrared to the submillimeter region using the same heterostructure material. Electrons streaming down a potential staircase sequentially emit photons at the steps. The latter consist of coupled quantum wells in which population inversion between discrete conduction band excited states is achieved in a 4-level atomic like laser scheme using tunneling injection. The AlInAs/GaInAs structure comprises 25 stages, each consisting of a graded gap n-type injection layer and a three coupled-well active region, cladded by waveguiding layers. The undoped active region includes 0.8 nm and 3.5 nm thick GaInAs wells separated by 3.5 nm AlInAs barriers. The reduced spatial overlap between the states of the laser transition and the strong tunnel-coupling to a nearby 2.8 nm GaInAs well ensure population inversion. A dramatic narrowing of the emission spectrum and attendant order of magnitude increase of the optical power above a current threshold = 10 kA/cm2 provide direct evidence of laser action. Powers = 20 mW in pulsed operation have been obtained at 80 K. Operating temperatures up to 125 K have been achieved with 5 mW of power. An outstanding feature of this laser is that the gain is much less sensitive to temperature than conventional semiconductor lasers. A detailed study of the temperature dependence of the threshold indicates a To = 125 K. In addition, the intrinsic linewidth of these lasers is expected to be Schawlow-Townes limited, similar to atomic lasers, without the linewidth enhancement factor typical of diode lasers. For a preliminary account of the operation of this laser at 10 K see Ref. 2.
<title>Characteristics of a ferroelectric liquid crystal spatial light modulator with a dielectric mirror</title> (1991)

The continuous gray scale operating characteristics of a ferroelectric liquid crystal spatial light modulator (FLC-SLM) are described. Then an FLC-SLM having a dielectric mirror between an a-Si:H photoconductor and an FLC light modulatory material is presented, and its operating characteristics are reported. The FLC-SLM having a dielectric mirror allows for continuous gray scale applications. It exhibits a resolution of 80 to 100 lp/mm and a higher optical gain than the device without a dielectric mirror.
New antibiotic U-64846: Fermentation, isolation and characterization. (1984)

Antibiotic U-64846 is a new entity with the molecular formula C18H35C1N4O9 (MW 486). It is a very water soluble, reddish solid which decomposes above 300 degrees C and which is air-sensitive. The antibiotic is produced by Streptomyces braegensis and it inhibits a variety of Gram-positive bacteria. Acidic hydrolysis gave 3,7-diaminoheptanoic acid. The antibiotic gives 1H NMR, 13C NMR, IR and UV spectra which indicate it is not closely related to known antibiotic families.
Advances and surgical decision‐making for breast reconstruction (2006)

In patients who undergo breast reconstruction after mastectomy, choosing the appropriate timing and the best method of reconstruction are essential to optimize outcomes and to minimize the potential for postoperative complications. At The University of Texas M. D. Anderson Cancer Center, the clinicopathologic factors that are used in the surgical decision-making for breast reconstruction after mastectomy include the breast cancer stage, status of axillary sentinel lymph node, smoking status, body habitus, preexisting scars, prior radiation therapy, and planned or previous chemotherapy. Immediate breast reconstruction after mastectomy is preferable for patients who have a low risk of requiring postmastectomy radiation therapy (PMRT) (Stage I breast cancer). Delayed reconstruction may be preferable in patients who are deemed preoperatively to require PMRT (Stage III breast cancer) to avoid difficulties associated with radiation delivery after an immediate breast reconstruction. In patients who are deemed preoperatively to be at an increased risk of requiring PMRT (Stage II breast cancer), delayed-immediate breast reconstruction may provide an additional option. The approach to breast reconstruction will need to be adapted to maintain an appropriate balance between minimizing the risk of recurrence and providing the best possible aesthetic outcomes as the indications for PMRT and other treatment modalities continue to change.
Nuclear Magnetic Resonance Gyroscope: For DARPA’s Micro-Technology for Positioning, Navigation and Timing Program (2013)

The navigation grade micro Nuclear Magnetic Resonance Gyroscope (µNMRG) being developed by Northrop Grumman is currently in the fourth and final phase of the DARPA-MTO Navigation Grade Integrated Micro Gyro (NGIMG) task as part of the Micro-Technology for Positioning, Navigation and Timing (micro-PNT) program. The µNMRG technology is pushing the boundaries of size, weight, power, and performance of rotation sensor technology, allowing new small platform applications of navigation grade Inertial Navigation System (INS) technology. The µNMRG technology has no moving parts, and the magnetic resonance process at the heart of the sensor is inherently vibration and acceleration insensitive. This makes it an ideal match for small platform high dynamics applications. The Phase 4 physics package is 10cm3 in volume for a single axis and is anticipated to meet the final NGIMG performance goals of 0.001°/?hr angle random walk, 0.01°/hr bias instability, greater than 500°/s full scale rate, and less than 50ppm scale factor stability. Information on the sensor basics of operation, task performance goals, current status, and demonstrated performance in testing at Northrop Grumman as well as independent testing at the U.S. Army Aviation and Missile Research Development and Engineering Center (AMRDEC) will be presented.
Molecular biology and genetics of prion diseases (1994)

Scrapie was thought for many years to be caused by a virus. Enriching fractions from Syrian hamster (SHa) brain for scrapie infectivity led to the discovery of the prion protein (PrP). To date, no scrapie-specific nucleic acid has been found. As well as scrapie, prion diseases include bovine spongiform encephalopathy (BSE) of cattle, as well as Creutzfeldt-Jakob disease (CJD) and Gerstmann-Sträussler-Scheinker syndrome (GSS) of humans. Transgenic (Tg) mice expressing both SHa and mouse (Mo) PrP genes were used to probe the molecular basis of the species barrier and the mechanism of scrapie prion replication. The prion inoculum was found to dictate which prions are synthesized de novo, even though the cells express both PrP genes. Discovery of mutations in the PrP genes of humans with GSS and familial CJD established that prion diseases are both genetic and infectious. Tg mice expressing MoPrP with the GSS point mutation spontaneously develop neurologic dysfunction, spongiform degeneration and astrocytic gliosis. Inoculation of brain extracts prepared from these Tg(MoPrP-P101L) mice produced neurodegeneration in many of the recipient animals after prolonged incubation times. These and other results suggest that prions are devoid of foreign nucleic acid and are thus different from viruses and viroids. Studies on the structure of PrPSc and PrPC suggest that the difference is conformational. Whether one or more putative alpha-helices in PrPC are converted into beta-sheets during synthesis of PrPSc is unknown. Distinct prion isolates or 'strains' exhibit different patterns of PrPSc accumulation which are independent of incubation times. Whether variations in PrPSc conformation are responsible for prion diversity remains to be established. Prion studies have given new insights into the etiologies of infectious, sporadic and inherited degenerative diseases.
Three-dimensional hole transport in nickel oxide by alloying with MgO or ZnO (2015)

It has been shown previously that the movement of a hole in nickel oxide is confined to two dimensions, along a single ferromagnetic plane. Such confinement may hamper hole transport when NiO is used as a p-type transparent conductor in various solar energy conversion technologies. Here, we use the small polaron model, along with unrestricted Hartree-Fock and complete active space self-consistent field calculations to show that forming substitutional MxNi1−xO alloys with M = Mg or Zn reduces the barrier for movement of a hole away from the ferromagnetic plane to which it is confined. Such reduction occurs for hole transfer alongside one or two M ions that have been substituted for Ni ions. Furthermore, the Mg and Zn ions do not trap holes on O sites in their vicinity, and NiO's transparency is preserved upon forming the alloys. Thus, forming MxNi1−xO alloys with M = Mg or Zn may enhance NiO's potential as a p-type transparent conducting oxide, by disrupting the two-dimensional confinement of holes in pure NiO.
Phase-noise characterization of optoelectronic components by carrier suppression techniques (2002)

Summary form only given. Phase noise of the optoelectronic components in a fiber-optic system represents a fundamental limit to achievable performance. This limit is not typically approached in signal transmission systems, because even reference signals have noise exceeding the noise of a photonic link. However, the optoelectronic device noise represents a limit for the achievable performance of the optoelectronic oscillator (OEO) and similar devices designed to photonically produce spectrally pure and stable references. In this paper, we propose a novel approach to characterize the phase noise of optoelectronic components.
<title>Ultrafast superconducting single-photon optical detectors</title> (2003)

We present a new class of single-photon devices for counting of both visible and infrared photons. Our superconducting single-photon detectors (SSPDs) are characterized by the intrinsic quantum efficiency (QE) reaching up to 100%, above 10 GHz counting rate, and negligible dark counts. The detection mechanism is based on the photon-induced hotspot formation and subsequent appearance of a transient resistive barrier across an ultrathin and submicron-wide superconducting stripe. The devices are fabricated from 3.5-nm-thick NbN films and operate at 4.2 K, well below the NbN superconducting transition temperature. Various continuous and pulsed laser sources in the wavelength range from 0.4 μm up to >3 μm were implemented in our experiments, enabling us to determine the detector QE in the photon-counting mode, response time, and jitter. For our best 3.5-nm-thick, 10×10 μm<sup>2</sup>-area devices, QE was found to reach almost 100% for any wavelength shorter than about 800 nm. For longer-wavelength (infrared) radiation, QE decreased exponentially with the photon wavelength increase. Time-resolved measurements of our SSPDs showed that the system-limited detector response pulse width was below 150 ps. The system jitter was measured to be 35 ps. In terms of the counting rate, jitter, and dark counts, the NbN SSPDs significantly outperform their semiconductor counterparts. Already identifeid and implemented applications of our devices range from noninvasive testing of semiconductor VLSI circuits to free-space quantum communications and quantum cryptography.
Transcytosis of <i>Junonia coenia</i> densovirus VP4 across the gut epithelium of <i>Spodoptera frugiperda</i> (Lepidoptera: Noctuidae) (2018)

The Junonia coenia densovirus rapidly traverses the gut epithelium of the host lepidopteran without replicating in the gut cells. The ability of this virus to transcytose across the gut epithelium is of interest for the potential use of virus structural proteins as delivery vehicles for insecticidal peptides that act within the insect hemocoel, rather than in the gut. In this study, we used fall armyworm, Spodoptera frugiperda to examine the binding of the virus to brush border membrane vesicle proteins by two-dimensional ligand blot analysis. We also assessed the rate of flux of the primary viral structural protein, VP4 fused to eGFP with a proline-rich linker (VP4-P-eGFP) through the gut epithelium ex vivo in an Ussing chamber. The mechanisms involved with transcytosis of VP4-P-eGFP were assessed by use of inhibitors. Bovine serum albumin (BSA) and eGFP were used as positive and negative control proteins, respectively. In contrast to BSA, which binds to multiple proteins on the brush border membrane, VP4-P-eGFP binding was specific to a protein of high molecular mass. Protein flux was significantly higher for VP4-P-eGFP after 2 h than for albumin or eGFP, with rapid transcytosis of VP4-P-eGFP within the first 30 min. In contrast to BSA which transcytosed following clathrin-mediated endocytosis, the movement of VP4-P-eGFP was vesicle-mediated but clathrin-independent. The specificity of binding combined with the efficiency of transport across the gut epithelium suggest that VP4 will provide a useful carrier for insecticidal peptides active within the hemocoel of key lepidopteran pests including S. frugiperda.
Camera Calibration with a Transparent Calibration Tool Using Color Filters: Application to Stereo Camera Calibration for a Distant Object (2006)

In this paper, we propose a transparent calibration tool that can calibrate in a straightforward manner without resetting or removing the tool, which consists of two parallel transparent boards with patterns of dots of a color filter material. The tool is installed in front of a color camera, which acquires images through it. Images for calibration and the scene image are acquired simultaneously in different color bands. The proposed method is applied to stereo camera calibration for a distant small object
Enterprise JavaBeans caching in clustered environments (2005)

Abstract We present the design of an Enterprise JavaBeans (EJBs) caching architecture, and show that EJB caching can greatly improve application throughput in clustered environments. Throughput is improved because data serving is offloaded from the database server to the cache‐enabled application server. EJB caching is successful because it exploits the low‐latency connections between the database server and application servers that exist in a clustered environment. An important feature of our architecture is that the caching function is transparent to applications that use it. The cache‐enabled application server uses the same (EJB) programming model, and the same transactional semantics, as provided by non‐caching architectures. Copyright © 2005 John Wiley & Sons, Ltd.
Boosting video classification using cross-video signals (2011)

We consider the problem of large-scale video classification. Our attention is focused on online video services since they can provide rich cross-video signals derived from user behavior. These signals help us to extract correlated information across videos which are co-browsed, co-uploaded, co commented, co-queried, etc. Majority of the video classification methods omit this rich information and focus solely on a single test instance. In this paper, we propose a video classification system that exploits various cross-video signals offered by large-scale video databases. In our experiments, we show up to 4.5% absolute equal error rate (17% relative) improvement over the baseline on four video classification problems.
ChemInform Abstract: Late‐Stage Fluorination: Fancy Novelty or Useful Tool? (2015)

Abstract Review: [24 refs.
Gut microbiome development along the colorectal adenoma–carcinoma sequence (2015)

Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gut microbe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions enriched in each group. An analysis of potential risk factors indicates that high intake of red meat relative to fruits and vegetables appears to associate with outgrowth of bacteria that might contribute to a more hostile gut environment. These findings suggest that faecal microbiome-based strategies may be useful for early diagnosis and treatment of colorectal adenoma or carcinoma.