gebhart/patrepeval huggingface dataset:
Evaluation of RAPD analysis for identification of polymorphisms in canine genomic DNA (1997)

Abstract Random amplified polymorphic DNA (RAPD) analysis was assessed as a method to identify polymorphic markers in dogs for potential use in linkage analysis of traits segregating in specific pedigrees. Three sets of primers were evaluated: 294 ten‐nucleotide long arbitrary primers from sets commonly used in RAPD analysis; 40 primers containing simple repeat elements; and 10 long random primers (19‐24 nucleotides). Of the 294 10‐mer RAPD primers, 220 (75%) amplified DNA segments from template DNA yielding primarily of 4‐5 DNA bands. Furthermore, only a few of the primers containing simple repeat elements produced discrete DNA fragments on amplification. On the other hand, all ten of the longer primers yielded amplification products with an average of 10 bands. Polymorphic bands were identified among the test DNA samples in 30% of reactions using 10‐mer RAPD primers, and in 50% of cases utilizing the long primers. RAPD primers with higher GC content amplified more polymorphic DNA fragments. Characteristic differences in amplification patterns were noted among breeds with several of these primers. We conclude from this study that by selecting primers with high GC content RAPD analysis can be successfully applied to identify polymorphic markers even in relatively inbred dog populations, and offers a promising method to search for markers linked to genetic traits of interest.
A Resource Management System for Interference Mitigation in Enterprise OFDMA Femtocells (2012)

To meet the capacity demands from ever-increasing mobile data usage, mobile network operators are moving toward smaller cell structures. These small cells, called femtocells, use sophisticated air interface technologies such as orthogonal frequency division multiple access (OFDMA). While femtocells are expected to provide numerous benefits such as energy efficiency and better throughput, the interference resulting from their dense deployments prevents such benefits from being harnessed in practice. Thus, there is an evident need for a resource management solution to mitigate the interference that occurs between collocated femtocells. In this paper, we design and implement one of the first resource management systems, FERMI, for OFDMA-based femtocell networks. As part of its design, FERMI: 1) provides resource isolation in the frequency domain (as opposed to time) to leverage power pooling across cells to improve capacity; 2) uses measurement-driven triggers to intelligently distinguish clients that require just link adaptation from those that require resource isolation; 3) incorporates mechanisms that enable the joint scheduling of both types of clients in the same frame; and 4) employs efficient, scalable algorithms to determine a fair resource allocation across the entire network with high utilization and low overhead. We implement FERMI on a prototype four-cell WiMAX femtocell testbed and show that it yields significant gains over conventional approaches.
New strategies for the prevention and treatment of Helicobacter pylori infection (2002)

Helicobacter pylori infects the stomach of > 50% of the human population worldwide, with higher prevalence in the developing countries. A strict correlation between H. pylori infection and gastroduodenal diseases has been demonstrated, including gastritis, peptic ulcer and gastric cancer. Current therapies against H. pylori consist of an antisecretory plus antibiotics. These therapies are effective in 80 - 90% of the cases; presently, no alternative therapies have been shown to give comparable or better results. There are two main reasons for therapy failure: poor compliance, which results in cure discontinuation, and antibiotic resistance. To overcome the drawbacks inherent to any antibiotic therapy, a prophylactic vaccine seems to be the most reasonable approach. Vaccines have been developed based on data obtained in animal models, a number of which are currently in Phase I clinical trials, in some cases giving encouraging data for safety and immunogenicity. In the absence of any immunological correlate of protection against H. pylori, it will be possible to evaluate the efficacy of these vaccines only in large Phase III clinical trials.
Simple enrichment and analysis of plasma lysophosphatidic acids (2013)

A simple and highly efficient technique for the analysis of lysophosphatidic acid (LPA) subspecies in human plasma is described. The streamlined sample preparation protocol furnishes the five major LPA subspecies with excellent recoveries. Extensive analysis of the enriched sample reveals only trace levels of other phospholipids. This level of purity not only improves MS analyses, but enables HPLC post-column detection in the visible region with a commercially available fluorescent phospholipids probe. Human plasma samples from different donors were analyzed using the above method and validated by LC-ESI/MS/MS.
Geometric accuracy in airborne SAR images (1989)

Uncorrected across-track motions of a synthetic aperture radar (SAR) platform can cause both a severe loss of azimuthal positioning accuracy in, and defocusing of, the resultant SAR image. It is shown how the results of an autofocus procedure can be incorporated in the azimuth processing to produce a fully focused image that is geometrically accurate in azimuth. Range positioning accuracy is also discussed, leading to a comprehensive treatment of all aspects of geometric accuracy. The system considered is an X-band SAR.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Nonmydriatic fluorescence-based quantitative imaging of human macular pigment distributions (2006)

We have developed a CCD-camera-based nonmydriatic instrument that detects fluorescence from retinal lipofuscin chromophores ("autofluorescence") as a means to indirectly quantify and spatially image the distribution of macular pigment (MP). The lipofuscin fluorescence intensity is reduced at all retinal locations containing MP, since MP has a competing absorption in the blue-green wavelength region. Projecting a large diameter, 488 nm excitation spot onto the retina, centered on the fovea, but extending into the macular periphery, and comparing lipofuscin fluorescence intensities outside and inside the foveal area, it is possible to spatially map out the distribution of MP. Spectrally selective detection of the lipofuscin fluorescence reveals an important wavelength dependence of the obtainable image contrast and deduced MP optical density levels, showing that it is important to block out interfering fluorescence contributions in the detection setup originating from ocular media such as the lens. Measuring 70 healthy human volunteer subjects with no ocular pathologies, we find widely varying spatial extent of MP, distinctly differing distribution patterns of MP, and strongly differing absolute MP levels among individuals. Our population study suggests that MP imaging based on lipofuscin fluorescence is useful as a relatively simple, objective, and quantitative noninvasive optical technique suitable to rapidly screen MP levels and distributions in healthy humans with undilated pupils.
Cross-linked stable second-order nonlinear optical polymer by photochemical reaction (1991)

A new method for obtaining cross-linked second-order nonlinear optical polymer by photochemical reaction has been described. An active dye was processed and poled in a photoreactive polymer in a manner similar to doped polymer system, and photo-cross-linked in the poled phase by ultraviolet irradiation. The dye doped (20% by weight) cross-linked polymer has a nonlinear optical coefficient d33 of 5.1 pm/V at 1.540 μm and shows no relaxation after being subjected to thermal treatment at 60 °C for 0.5 h.
Alternative application-specific processor architectures for fast arbitrary bit permutations (2008)

Block ciphers are used to encrypt data and provide data confidentiality. For interoperability reasons, it is desirable to support a variety of block ciphers efficiently. Of the basic operations in block ciphers, only bit permutation is very slow on existing processors, followed by integer multiplication. Although new permutation instructions proposed recently can accelerate bit permutations in general-purpose processors, reducing the number of instructions needed to achieve an arbitrary n-bit permutation from O(n) to O(log2n), the data dependency between permutation instructions prevents them from being executed in fewer than log2n cycles, even on superscalar processors. Since Application-Specific Instruction-Set Processors (ASIPs) have fewer constraints on maintaining standard processor datapath and control conventions, six alternative ASIP approaches are proposed in this paper to achieve arbitrary 64-bit permutations in one or two cycles without increasing the cycle time. These approaches use new BFLY and IBFLY instructions. We also compare these approaches and their efficiency in performing arbitrary 64-bit permutations.
Detection of extracellular matrix modification in cancer models with inverse spectroscopic optical coherence tomography (2016)

In cancer biology, there has been a recent effort to understand tumor formation in the context of the tissue microenvironment. In particular, recent progress has explored the mechanisms behind how changes in the cell-extracellular matrix ensemble influence progression of the disease. The extensive use of in vitro tissue culture models in simulant matrix has proven effective at studying such interactions, but modalities for non-invasively quantifying aspects of these systems are scant. We present the novel application of an imaging technique, Inverse Spectroscopic Optical Coherence Tomography, for the non-destructive measurement of in vitro biological samples during matrix remodeling. Our findings indicate that the nanoscale-sensitive mass density correlation shape factor D of cancer cells increases in response to a more crosslinked matrix. We present a facile technique for the non-invasive, quantitative study of the micro- and nano-scale structure of the extracellular matrix and its host cells.
A Greedy Scheme for Designing Delay Monitoring Systems of IP Networks (2008)

Though appendicitis is common many important questions remain unanswered. When is the appendix normal and when is it the cause of abdominal pain? Why does appendicitis primarily affect older children and young adults? Why is appendicitis uncommon in those under five years of age and in those over sixty years of age? Why are boys affected more often than girls? Why does appendicitis appear to run in some families? Why is appendicitis more common in affluent parts of the world and rare in parts where poverty and poor hygiene are prevalent? The epidemiology of appendicitis is complex and its cause is not explained by any single factor. The peak incidence of appendicitis coincides with the age when the immune system is most efficient and the lymphoid follicles are at their maximum development. Could this implicate immunological factors in the pathogenesis and, therefore, the epidemiology of appendicitis? Obstruction of the lumen of the appendix is believed to be the trigger initiating the processes that culminate in inflammation of the appendix. Fecaliths are a specific cause of appendicitis in about one-third of specimens Their physical consistency varies from soft to hard concretions. The reported incidence of fecaliths depends on whether the data was obtained from intraoperative palpation of the organ, from histological analysis of operative specimens or from autopsy reports. It is suggested that vegetable matter entering the lumen of the appendix forms the nucleus around which glandular secretions in the lumen desicate to form the calculi In the other two-thirds of instances where fecaliths are absent, the obstruction is thought to be caused by hypertrophy of mural lymphoid follicles in response to a host of causes that are discussed elsewhere in this book. This chapter aims to understand the environmental, demographic, cultural and genetic factors that make the appendix susceptible to obstruction and inflammation. To understand the epidemiology of appendicitis is to look at the possibility of moving beyond treating it operatively to entertaining non-operative treatments and to foresee a future when some cases of appendicitis can be prevented.
Forecasting uncertain events with small groups (2001)

We present a novel methodology for predicting future outcomes that uses small numbers of individuals participating in an imperfect information market. By determining their risk attitudes and performing a nonlinear aggregation of their predictions, we are able to assess the probability of the future outcome of an uncertain event and compare it to both the objective probability of its occurrence and the performance of the market as a whole. Experiments show that this nonlinear aggregation mechanism vastly outperforms both the imperfect market and the best of the participants.
A CONVENIENT PREPARATION OF 2-SUBSTITUTED 2-CYCLOPENTENONES FROM CYCLOPENTANONE USING 2-(MORPHOLINOTHIO)BENZOTHIAZOLE (1979)

Abstract 2-Substituted 2-cyclopentenones (4), a precursor of jasmonoids, were prepared in 47–77% overall yields from cyclopentanone (1) via 2-(2-benzothiazolylthio)cyclopentanone (2). Treatment of 1 with 2-(morpholinothio) benzothiazole gave 2 in 98% yield. Alkylation of 2 with RBr–K2CO3–KI–acetone followed by removal of the 2-mercaptobenzothiazole by thermolysis in benzene containing p-TsOH at 140 °C afforded (4) smoothly.
Radiomic Deformation and Textural Heterogeneity (R-DepTH) Descriptor to characterize Tumor Field Effect: Application to Survival Prediction in Glioblastoma (2021)

The concept of tumor field effect implies that cancer is a systemic disease with its impact way beyond the visible tumor confines. For instance, in Glioblastoma (GBM), an aggressive brain tumor, the increase in intracranial pressure due to tumor burden often leads to brain herniation and poor outcomes. Our work is based on the rationale that highly aggressive tumors tend to grow uncontrollably, leading to pronounced biomechanical tissue deformations in the normal parenchyma, which when combined with local morphological differences in the tumor confines on MRI scans, will comprehensively capture tumor field effect. Specifically, we present an integrated MRI-based descriptor, radiomic-Deformation and Textural Heterogeneity (r-DepTH). This descriptor comprises measurements of the subtle perturbations in tissue deformations throughout the surrounding normal parenchyma due to mass effect. This involves non-rigidly aligning the patients MRI scans to a healthy atlas via diffeomorphic registration. The resulting inverse mapping is used to obtain the deformation field magnitudes in the normal parenchyma. These measurements are then combined with a 3D texture descriptor, Co-occurrence of Local Anisotropic Gradient Orientations (COLLAGE), which captures the morphological heterogeneity within the tumor confines, on MRI scans. R-DepTH, on N = 207 GBM cases (training set (St) = 128, testing set (Sv) = 79), demonstrated improved prognosis of overall survival by categorizing patients into low- (prolonged survival) and high-risk (poor survival) groups (on St, p-value = 0.0000035, and on Sv, p-value = 0.0024). R-DepTH descriptor may serve as a comprehensive MRI-based prognostic marker of disease aggressiveness and survival in solid tumors.
Mechanically Gated Electrical Switches by Creasing of Patterned Metal/Elastomer Bilayer Films (2014)

Strain-gated logic devices are important for the development of advanced flexible electronics. Using a dual-monolayer-promoted film-transfer technique, flexible multilayer structures capable of undergoing large compressive deformation are prepared. Formation of a crease in the gap between electrodes at a geometrically tunable strain leads to the formation of an electrical connection in a reversible and reproducible fashion. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Large scale storm outage management (2004)

This paper describes a process for improving information used by electric utilities for managing restoration of distribution facilities damaged by large-scale storms such as large-scale ice storms and hurricanes. The process is realized in the form of a decision support tool that utilizes the model of the distribution circuit layout, the placement of protective and switching devices and the location of customers to determine how crew resources should be allocated and managed for cost-effective storm outage management. Equipment damage predictions based on the severity and location of the weather are also used to predict where and to what extent circuit damage is likely to occur. Given crew availability and the maintenance crew requirement for each damage type, a storm outage algorithm predicts damage per feeder, area and region and calculates estimated time to restoration for each customer. After the storm hits additional information such as customer calls, switch status and field damage assessments are utilized by the storm outage algorithm to provide updated predictions of damage and estimated time to restore.
Effect of Mutations at Serines 1280–1283 on the Mitogenic and Transforming Activities of the Insulin-like Growth Factor I Receptor (1996)

The insulin-like growth factor I receptor (IGF-IR) controls the extent of cell proliferation in a variety of cell types by at least 3 different ways: it is mitogenic, it causes transformation, and it protects cells from apoptosis. Previous reports indicated that certain domains in the C terminus of the IGF-IR transmitted a transforming signal that is additional to and separate from the mitogenic signal. We have now mutated the four serine residues at 1280-1283 of the IGF-IR, and transfected the mutant receptor into R- cells. Cells expressing the mutant receptor are fully responsive to IGF-I mediated mitogenesis, but are not transformed (no colony formation in soft agar). Several downstream signal transducers are not affected by the mutation, again suggesting a separate pathway for transformation. The mutant receptor can act as a dominant negative for growth, but cannot induce apoptosis in cells with endogenous wild-type receptors.
Gesture studio (2013)

The prevalence of multi-touch devices opens the space for rich interactions. However, the complexity for creating multi-touch interactions hinders this potential. In this paper, we present Gesture Studio, a tool for creating multi-touch interaction behaviors by combining the strength of two distinct but complementary approaches: programming by demonstration and declaration. We employ an intuitive video-authoring metaphor for developers to demonstrate touch gestures, compose complicated behaviors, test these behaviors in the tool and export them as source code that can be integrated into the developers' project.
Abortive lytic Epstein&ndash;Barr virus replication in tonsil-B lymphocytes in infectious mononucleosis and a subset of the chronic fatigue syndrome (2012)

Abstract: A systematic 2001–2007 review of 142 chronic fatigue syndrome (CFS) patients identified 106 CFS patients with elevated serum IgG antibodies to the herpesviruses Epstein–Barr virus (EBV), cytomegalovirus, or human herpesvirus (HHV) 6 in single or multiple infections, with no other co-infections detected. We named these 106 patients group-A CFS. Eighty-six of these 106 group-A CFS patients (81%) had elevated EBV early antibody, early antigen (diffuse), serum titers. A small group of six patients in the group-A EBV subset of CFS, additionally, had repetitive elevated-serum titers of antibody to the early lytic replication-encoded proteins, EBV dUTPase, and EBV DNA polymerase. The presence of these serum antibodies to EBV dUTPase and EBV DNA polymerase indicated EBV abortive lytic replication in these 6 CFS patients. None of 20 random control people (age- and sex-matched, with blood drawn at a commercial laboratory) had elevated serum titers of antibody to EBV dUTPase or EBV DNA polymerase ( P < 0.01). This finding needs verification in a larger group of EBV CFS subset patients, but if corroborated, it may represent a molecular marker for diagnosing the EBV subset of CFS. We review evidence that EBV abortive lytic replication with unassembled viral proteins in the blood may be the same in infectious mononucleosis (IM) and a subset of CFS. EBV-abortive lytic replication in tonsil plasma cells is dominant in IM. No complete lytic virion is in the blood of IM or CFS patients. Complications of CFS and IM include cardiomyopathy and encephalopathy. Circulating abortive lytic-encoded EBV proteins (eg, EBV dUTPase, EBV DNA polymerase, and others) may be common to IM and CFS. The intensity and duration of the circulating EBV-encoded proteins might differentiate the IM and EBV subsets of CFS. Abortive lytic replication may be a pathogenic mechanism for EBV disease. EBV (HHV4) is a gamma herpesvirus composed of dsDNA about 170 Kb in length. For this discussion, there are early genes (including expressions of encoded proteins EBV dUTPase, DNA polymerase, and nuclear proteins) and late genes (including expressions of capsid and membrane proteins). Abortive infection infers incomplete virion expressions of either early or late proteins, but the virion is incomplete. The lytic virus infers a complete virion. The pathologic consequences of EBV abortive replication are currently being investigated by authors. Keywords: Epstein–Barr virus, chronic fatigue syndrome, subset chronic fatigue syndrome, abortive lytic replication