gebhart/patrepeval huggingface dataset:
Herpes simplex virus type 2 tegument proteins contain subdominant T-cell epitopes detectable in BALB/c mice after DNA immunization and infection (2009)

Cytotoxic T cells are important in controlling herpes simplex virus type 2 (HSV-2) reactivation and peripheral lesion resolution. Humans latently infected with HSV-2 have cytotoxic T cells directed against epitopes present in tegument proteins. Studies in mice of immunity to HSV have commonly focused on immunodominant responses in HSV envelope glycoproteins. These antigens have not proved to be an effective prophylactic vaccine target for most of the human population. The murine immune response against HSV tegument proteins has not been explored. We analysed cellular responses in BALB/c mice directed against the tegument proteins encoded by UL46, UL47 and UL49 and against the envelope glycoprotein gD after DNA vaccination or HSV-2 infection. After DNA vaccination, the splenocyte T-cell response to overlapping peptides from UL46 and UL47 was more than 500 gamma interferon spot-forming units per 10(6) responder cells. Peptide truncation studies, responder cell fractionation and major histocompatibility complex binding studies identified several CD8(+) and CD4(+) epitopes. Cellular responses to tegument protein epitopes were also detected after HSV-2 infection. Tegument proteins are rational candidates for further HSV-2 vaccine research.
The Frankencamera (2010)

Although there has been much interest in computational photography within the research and photography communities, progress has been hampered by the lack of a portable, programmable camera with sufficient image quality and computing power. To address this problem, we have designed and implemented an open architecture and API for such cameras: the Frankencamera. It consists of a base hardware specification, a software stack based on Linux, and an API for C++. Our architecture permits control and synchronization of the sensor and image processing pipeline at the microsecond time scale, as well as the ability to incorporate and synchronize external hardware like lenses and flashes. This paper specifies our architecture and API, and it describes two reference implementations we have built. Using these implementations we demonstrate six computational photography applications: HDR viewfinding and capture, low-light viewfinding and capture, automated acquisition of extended dynamic range panoramas, foveal imaging, IMU-based hand shake detection, and rephotography. Our goal is to standardize the architecture and distribute Frankencameras to researchers and students, as a step towards creating a community of photographer-programmers who develop algorithms, applications, and hardware for computational cameras.
Molecular genetics of prostate cancer: new prospects for old challenges (2010)

Despite much recent progress, prostate cancer continues to represent a major cause of cancer-related mortality and morbidity in men. Since early studies on the role of the androgen receptor that led to the advent of androgen deprivation therapy in the 1940s, there has long been intensive interest in the basic mechanisms underlying prostate cancer initiation and progression, as well as the potential to target these processes for therapeutic intervention. Here, we present an overview of major themes in prostate cancer research, focusing on current knowledge of principal events in cancer initiation and progression. We discuss recent advances, including new insights into the mechanisms of castration resistance, identification of stem cells and tumor-initiating cells, and development of mouse models for preclinical evaluation of novel therapuetics. Overall, we highlight the tremendous research progress made in recent years, and underscore the challenges that lie ahead.
Purification and partial characterization of a receptor protein for mouse interferon gamma. (1988)

A receptor protein for mouse interferon gamma has been purified from solubilized plasma membranes of the mouse monomyelocytic cell line WEHI-3. Sequential wheat germ agglutinin and ligand affinity chromatography of membranes extracted with octyl beta-D-glucopyranoside resulted in at least a 680-fold purification of the receptor, as measured by precipitating it in association with liposomes composed of phosphatidylcholine. The purified receptor bound 125I-labeled recombinant mouse interferon gamma (rMuIFN-gamma) with a Kd of 10 nM, a value comparable to that obtained with isolated membranes (3.5 nM). PAGE analysis of radiolabeled (with either 35S or 125I) receptor preparations consistently revealed a major band of 95 kDa. This species was degraded with time to smaller fragments, principally one of 60 +/- 5 kDa. Treatment with peptide:N-glycosidase F reduced the apparent molecular masses of the proteins in the 95- and 60-kDa regions by 15-20 kDa each. GR-20, a monoclonal antibody against the receptor, completely inhibited specific binding of 125I-labeled rMuIFN-gamma to WEHI-3 cells, blocked the induction of priming by rMuIFN-gamma of macrophage-mediated tumor cell killing, removed binding activity for 125I-labeled rMuIFN-gamma from solubilized membranes, and immunoprecipitated a single 95-kDa protein from the extract of surface labeled (125I) WEHI-3 cells. Cross-linking of 125I-labeled rMuIFN-gamma to its receptor yielded a complex of 125 +/- 5 kDa, consistent with the binding of the dimeric form of mouse interferon gamma (32 kDa) to a membrane protein of 95 kDa. These data suggest that the receptor for mouse interferon gamma (or a ligand-binding subunit thereof) is a glycoprotein of 95 kDa.
Selective removal of low density lipoprotein by plasmapheresis in familial hypercholesterolemia. (1985)

Plasma lipoproteins were selectively removed from familial hypercholesterolemic patients by using two types of plasmapheresis: double-membrane filtration and selective adsorption of very low density lipoproteins (VLDL) and low density lipoproteins (LDL). In both techniques, plasma was separated from blood cells by using hollow-fiber filters, and 100% of the VLDL and LDL was recovered in the filtrate. In double-membrane filtration, the second hollow-fiber filter trapped 84% of LDL + VLDL, 48% of high density lipoprotein (HDL), 24% of albumin, and 46% of the remaining plasma protein. By treating 3 liters of plasma from a patient weighing 60 kg, 60% of the LDL and 30% to 40% of the HDL were removed as a result of an exponential decay of each component with the respective trapping coefficients. When dextran sulfate-cellulose was used as a LDL sorbent, there was only loss of LDL and VLDL, and no loss of any other major plasma component or of HDL. The sorbent column (400 ml) was saturated with 7.5 g of LDL cholesterol by treatment with 3.5 liters of plasma; the maximum reduction of LDL cholesterol was thus about 300 mg/dl for the patient weighing 60 kg. No serious side effects were observed during the long-term trials (19 to 27 months for four patients on double-membrane filtration and 10 months for the two patients on dextran sulfate-cellulose treatment.
Relationship Between Structure and Mechanical Function of the Tissues of the Intervertebral Joint (2000)

This paper reviews our current understanding of the relationship between the structures and properties of the tissues of the spine and their mechanical functions. Emphasis is on the human lumbar spine. Vertebrae consist of a core of cancellous bone (low density) surrounded by a shell of cortical bone (high stiffness); as a result they have high stiffness but low mass. The intervertebral disc is able to withstand compression because of the swelling pressure exerted by the nucleus pulposus which is constrained, radially, by the annulus fibrosus. Thus the disc acts as a thick-walled pressure vessel. Collagen fibers within the annulus provide reinforcement during compression, bending and torsion of the disc. Collagen fibers also provide tensile reinforcement and prevent tears spreading across ligaments. The ligamenta flava contain elastic fibers (low stiffness and low strength) with collagen fibers (high stiffness and high strength). In the unstretched ligamenta flava, the collagen fibers have almost random orientations but they become aligned as the ligament is stretched. This structure enables the high extensibility of elastic fibers to be exploited but protects them from damage at high strains. The structure of the interspinous ligament suggests that its main function is to attach the thoracolumbar fascia to the posterior spine. Thus the fascia is maintained in tension when stretched by the abdominal muscles. This and other observations indicate the importance of muscles for maintaining the stability of the spinal column.
Firing Patterns of Human Genioglossus Motor Units During Voluntary Tongue Movement (2006)

The tongue participates in a range of complex oromotor behaviors, including mastication, swallowing, respiration, and speech. Previous electromyographic studies of the human tongue have focused on respiratory-related tongue muscle activities and their role in maintaining upper airway patency. Remarkably, the activities of human hypoglossal motor units have not been studied during the execution of voluntary maneuvers. We recorded single motor unit activity using tungsten microelectrodes in the genioglossus muscle of 10 healthy human subjects performing both slow tongue protrusions and a static holding maneuver. Displacement of the tongue was detected by an isotonic transducer coupled to the lingual surface through a customized lever arm. For protrusion trials, the firing rate at recruitment was 13.1 +/- 3 Hz and increased steeply to an average of 24 +/- 6 Hz, often with very modest increases in tongue protrusion. For the static holding task, the average firing rate was 16.1 +/- 4 Hz, which is surprisingly high relative to limb motor units. The average coefficient of variation of interspike intervals was approximately 20% (range, 10-28%). These are the first recordings of their type obtained in human subjects and provide an initial glimpse into the voluntary control of hypoglossal motoneurons during tongue movements presumably instigated by activity in the motor cortex.
REPRESENTASI KECANTIKAN WANITA INDONESIA PADA COVER MAJALAH FEMINA EDISI TAHUNAN 2014 DAN MAJALAH KARTINI EDISI JANUARI 2014 (2014)

Dewasa ini, kecantikan wanita terbentuk dari berbagai standar yang merupakan hasil dari pengaruh modernisme dan diakui oleh sebagian besar wanita di Indonesia sebagai hal yang mainstream . Selain itu, kehadiran post-modernisme saat ini yang memiliki konsep pemikiran substream membuat standar kecantikan mainstream tampak menjadi kabur. Namun pada akhirnya, kecantikan substream itu tetap harus mengikuti standar mainstream agar dapat diterima oleh masyarakat. Hal ini ditampilkan pada cover kedua majalah wanita Indonesia ternama yaitu majalah Femina di edisi tahunan 2014 dan majalah Kartini di edisi Januari 2014. Dengan menggunakan Visual Methodologies , teori semiologi,  post-modernism, dan  nirmana, penelitian ini mengungkapkan bagaimana kedua majalah tersebut menjadi bagian dari fenomena kecantikan mainstream yang menerima kecantikan substream dan menjadi tren yang disukai oleh masyarakat luas.
Hypoglycemia in adults. (1999)

Hypoglycemia is a clinical and biological syndrome, caused by an abnormal decrease in plasma glucose levels to below 0.55 g/l (3.0 mmol/l). Hypoglycemia is responsible for non-specific signs and symptoms which should be noted in a particular pathological context, and for secretion of counterregulatory hormones (mainly glucagon and catecholamines). Difficulty in identifying the etiology is variable, based upon history and physical examination, and hormonal investigations or imaging procedures, according to the results. Drug-related hypoglycemia is the most frequent observed cause (mainly in insulin-treated diabetic patients, but many drugs may be involved), followed par toxicity (alcohol mainly). Tumor-induced hypoglycemia is secondary to inappropriate insulin secretion by a beta-cell pancreatic tumor (insulinoma), and, rarely to an extrapancreatic mesenchymal large tumor secreting IGF-II. Hypoglycemia is present in other diseases, such as hormonal deficiencies, hepatic, or renal failure, or acute cardiac insufficiency. Multifactorial hypoglycemia seems to be underdiagnosed, mainly in hospitalized, underfed older patients with severe disease or sepsis. Autoimmune hypoglycemia is rare, due to insulin or insulin-receptor autoantibodies. Reactive hypoglycemia is observed after gastrectomy, but true primitive hypoglycemia appears to be rare, with false excess diagnosis in the majority of the cases.
Sensing Techniques for Multi-Device Interfaces (2003)

As computing becomes more and more ubiquitous, there has been a trend for computing resources to become fragmented into small, specialized pieces: from mainframes, to personal computers, to an explosion of tablet computers, handheld devices, cell phones, pagers, wrist watches, and ear buds. Yet wireless networking acts as a medium that potentially can tie all of these pieces back together, enabling users to dynamically combine multiple devices to provide new capabilities that otherwise would not be possible. Jeff Pierce has a wonderful phrase for this vision of dynamically forming multi-device interfaces: opportunistic annexing [12]. In short, wireless networking will lead technology in entirely new directions that are difficult to foresee: in 100 years, I expect the phrase wireless networking will sound a lot like the phrase horseless carriage does to us now. This proposal contributes to workshop goal (2), enabling software and architectures, as well as This proposal contributes to workshop goal (2), enabling software and architectures, as well as goal (3), the design of multi-device interfaces, in two significant ways. First we discuss the general strategy of recognizing synchronous gestures as an approach that can allow users to intuitively form connections (associations) between distributed mobile devices. Forming meaningful sets of devices is a key challenge for opportunistic annexing. Second, we discuss how sensors might be used to sense when and how the user is employing multiple devices, and to sense transitions between active use (when the user is attending to the device), versus disuse, when the user may be ignoring or only partially attending to the device. Sensing such transitions may be essential if we are to design multi-device systems that do not distract user’s from their current tasks.
Retinal Imaging With Adaptive Optics Scanning Laser Ophthalmoscopy in Unexplained Central Ring Scotoma (2008)

Adaptive optics scanning laser ophthalmoscopy allows for noninvasive, in vivo visualization of retinal abnormalities at a cellular level. We herein describe for the first time, to our knowledge, the utility of high-resolution retinal imaging in studying the photoreceptor mosaic in an otherwise unexplained visual disturbance. Imaging of the cone mosaic was performed in a 64-year-old man with a unilateral ringlike paracentral distortion that could not be explained using common clinical imaging instruments. Adaptive optics scanning laser ophthalmoscopy findings revealed a parafoveal circular abnormality of the cone mosaic approximately 3 degrees in diameter that corresponded to the ring of visual disturbance. Visualization of the cone mosaic with adaptive optics scanning laser ophthalmoscopy can reveal photoreceptor damage that may not be detectable with standard imaging devices. Optical axial sectioning of the retina may help in identifying and localizing abnormalities within the retinal layers.
Multi-Organ toxicity demonstration in a functional human in vitro system composed of four organs (2016)

We report on a functional human model to evaluate multi-organ toxicity in a 4-organ system under continuous flow conditions in a serum-free defined medium utilizing a pumpless platform for 14 days. Computer simulations of the platform established flow rates and resultant shear stress within accepted ranges. Viability of the system was demonstrated for 14 days as well as functional activity of cardiac, muscle, neuronal and liver modules. The pharmacological relevance of the integrated modules were evaluated for their response at 7 days to 5 drugs with known side effects after a 48 hour drug treatment regime. The results of all drug treatments were in general agreement with published toxicity results from human and animal data. The presented phenotypic culture model exhibits a multi-organ toxicity response, representing the next generation of in vitro systems, and constitutes a step towards an in vitro "human-on-a-chip" assay for systemic toxicity screening.
Breathing New Life into Pneumonia Diagnostics (2009)

The date 2 November 2009 marked the first World Pneumonia Day, launched by a coalition of child health organizations to support global efforts to prioritize pneumonia treatment and prevention. Despite recent medical advances, pneumonia takes the lives of up to 2 million children under age 5 each year—more than AIDS, malaria, and measles combined (15). As with many other illnesses, the disease burden is greatest among the world's most vulnerable population: children living in developing nations. For every child who dies of pneumonia in a developed country, more than 2,000 die in developing countries (16).

With safe and effective vaccines against Haemophilus influenzae type b (Hib), Streptococcus pneumoniae, and measles virus and with improvements in environment and nutrition and in case management standards, we now have several strategies to both prevent and treat pneumonia. The challenge is to ensure universal access to these life-saving interventions.

Laboratory diagnostics and clinical microbiologists should play an important part in global efforts to prevent and treat pneumonia. Diagnostic testing has an essential role in ensuring the most appropriate and effective therapy for individual patients. It also plays a role in disease surveillance in defining the etiologic spectrum of pneumonia cases and deaths. This in turn forms the evidence base for strategic decisions by global decision makers (such as the World Health Organization, UNICEF, and the GAVI Alliance), vaccine manufacturers, and funders to develop and support treatment algorithms, vaccine products and programs, and other effective prevention strategies. World Pneumonia Day also reminds us that much work remains to be done in pneumonia diagnostics and that historically, even with the best of methods, we have been unable to define the microbial etiology of a significant proportion of pneumonia episodes, particularly in children. The conditions under which pneumonia mortality is greatest are also the conditions under which adequate diagnosis is least possible. Even in settings with access to state-of-the-art microbiological diagnosis, establishing the etiology of a pneumonia case is fundamentally vexed by the limited ability to obtain specimens from the site of infection without contamination by upper respiratory secretions. Lack of sensitive laboratory diagnostic tools has probably played a direct role in the delayed introduction of effective vaccines to prevent pneumonia. Vaccines against Hib and S. pneumoniae alone may prevent >50% of severe childhood pneumonia, but poor diagnostics contribute to substantial underdiagnosis, and thus, substantial efforts need to be put into place to build awareness about the potential impact of these interventions. In spite of these limitations, significant advances have been made in diagnostic technology. However, technology alone is not a panacea for pneumonia diagnostic needs: assessment of performance within clinical and epidemiologic contexts is essential.
Modification of Alternative Splicing by Antisense Therapeutics (2004)

Alternative splicing allows the production of several different proteins from a single pre-mRNA, resulting in an increased diversity of proteins derived from a relatively limited number of transcribed genes. Although it is necessary for normal development, alternative splicing and its aberrations are also implicated in disease states from thalassemia and cancer to neurodegenerative disorders. Techniques that trick the splicing machinery to alter the splicing pathways can be of high therapeutic value. Antisense technology, used mostly for RNA downregulation, recently has been adapted to alter the splicing process. The promise of this approach is now being realized as a result of chemical modification of oligonucleotides and improvements in their delivery in vivo.
Measuring coupling and cohesion of software modules: an information-theory approach (2002)

Coupling of a subsystem characterizes its interdependence with other subsystems. A subsystem's cohesion, on the other hand, characterizes its internal interdependencies. When used in conjunction with other attributes, measurements of a subsystem's coupling and cohesion can contribute to software quality models. An abstraction of a software system can be represented by a graph, and a module (subsystem) by a subgraph. Software design graphs depict components and their relationships. E.B. Allen and T.M. Khoshgoftaar (1999) proposed information theory-based measures of coupling and cohesion of a modular system. This paper proposes related information theory-based measures of coupling and cohesion of a module. These measures have the properties of module-level coupling and cohesion defined by Briand, Morasca and Basili (1997, 1999) . We define cohesion of a module in terms of intra-module coupling, normalized to between zero and one. We illustrate the measures with example graphs and an empirical analysis of the call graph of a moderate-sized C program, the Nethack computer game. Preliminary analysis showed that the information-theory approach has finer discrimination than counting.
Nuclear Import of Cdk/Cyclin Complexes: Identification of Distinct Mechanisms for Import of Cdk2/Cyclin E and Cdc2/Cyclin B1 (1999)

Reversible phosphorylation of nuclear proteins is required for both DNA replication and entry into mitosis. Consequently, most cyclin-dependent kinase (Cdk)/cyclin complexes are localized to the nucleus when active. Although our understanding of nuclear transport processes has been greatly enhanced by the recent identification of nuclear targeting sequences and soluble nuclear import factors with which they interact, the mechanisms used to target Cdk/cyclin complexes to the nucleus remain obscure; this is in part because these proteins lack obvious nuclear localization sequences. To elucidate the molecular mechanisms responsible for Cdk/cyclin transport, we examined nuclear import of fluorescent Cdk2/cyclin E and Cdc2/cyclin B1 complexes in digitonin-permeabilized mammalian cells and also examined potential physical interactions between these Cdks, cyclins, and soluble import factors. We found that the nuclear import machinery recognizes these Cdk/cyclin complexes through direct interactions with the cyclin component. Surprisingly, cyclins E and B1 are imported into nuclei via distinct mechanisms. Cyclin E behaves like a classical basic nuclear localization sequence-containing protein, binding to the alpha adaptor subunit of the importin-alpha/beta heterodimer. In contrast, cyclin B1 is imported via a direct interaction with a site in the NH2 terminus of importin-beta that is distinct from that used to bind importin-alpha.
Facts and Recommendations about Total Homocysteine Determinations: An Expert Opinion (2004)

This review is divided into two sections: (a) determination of homocysteine (methods and their performance, sample collection and handling, biological determinants, reference intervals, within-person variability, and methionine loading test); and (b) risk assessment and disease diagnosis (homocystinuria, folate and cobalamin deficiencies, cardiovascular disease, renal failure, psychiatric disorders and cognitive impairment, pregnancy complications and birth defects, and screening of elderly and newborns). Each of these subsections concludes with a separate series of recommendations to assist the clinician and the research scientist in making informed decisions. The review concludes with a list of unresolved questions.