gebhart/patrepeval huggingface dataset:
Active Learning for Anomaly and Rare-Category Detection (2004)

We introduce a novel active-learning scenario in which a user wants to work with a learning algorithm to identify useful anomalies. These are distinguished from the traditional statistical definition of anomalies as outliers or merely ill-modeled points. Our distinction is that the usefulness of anomalies is categorized subjectively by the user. We make two additional assumptions. First, there exist extremely few useful anomalies to be hunted down within a massive dataset. Second, both useful and useless anomalies may sometimes exist within tiny classes of similar anomalies. The challenge is thus to identify “rare category ” records in an unlabeled noisy set with help (in the form of class labels) from a human expert who has a small budget of datapoints that they are prepared to categorize. We propose a technique to meet this challenge, which assumes a mixture model fit to the data, but otherwise makes no assumptions on the particular form of the mixture components. This property promises wide applicability in real-life scenarios and for various statistical models. We give an overview of several alternative methods, highlighting their strengths and weaknesses, and conclude with a detailed empirical analysis. We show that our method can quickly zoom in on an anomaly set containing a few tens of points in a dataset of hundreds of thousands. 1
Supplementary Table from Venetoclax Cooperates with Ionizing Radiation to Attenuate Diffuse Midline Glioma Tumor Growth (2023)

Supplementary Table from Venetoclax Cooperates with Ionizing Radiation to Attenuate Diffuse Midline Glioma Tumor Growth
Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies (2000)

The three-dimensional structure of the anti-apoptotic protein Bcl-xL complexed to a 25-residue peptide from the death promoting region of Bad was determined using NMR spectroscopy. Although the overall structure is similar to Bcl-xL bound to a 16-residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl-xL. However, based upon site-directed mutagenesis experiments, these additional contacts do not account for the increased affinity of the Bad 25-mer for Bcl-xL compared to the Bad 16-mer. Rather, the increased helix propensity of the Bad 25-mer is primarily responsible for its greater affinity for Bcl-xL. Based on this observation, a pair of 16-residue peptides were designed and synthesized that were predicted to have a high helix propensity while maintaining the interactions important for complexation with Bcl-xL. Both peptides showed an increase in helix propensity compared to the wild-type and exhibited an enhanced affinity for Bcl-xL.
Major royal jelly proteins influence the neurobiological regulation of the division of labor among honey bee workers (2022)

Age-based division of labor among workers is a fundamental life-history trait of many social insects, including the Western honey bee, Apis mellifera L. Extensive studies of the causation of the most pronounced transition from performing tasks in the nest to outside foraging indicate hormonal regulation of complex physiological changes. However, the proximate neurobiological mechanisms that cause the behavioral repertoire to change are still not understood and require novel approaches to be fully characterized. Thus, we established the first comprehensive monoclonal antibody microarray in honey bees with 16,320 antibodies to directly identify proteins in the brain that regulate the transition to foraging. Major royal jelly protein (MRJP) 1 and MRJP3 were identified as potential protein effectors and further investigated. A series of experimental manipulations of the workers' behavioral transition led to changes in MRJP1 and MRJP3 quantities in accordance with their presumed functional role. Injection of MRJPs into the brain resulted in increased task-reversal from foraging to nursing and decreased task-progression from nursing to foraging, while the latter was increased by injection with MRJP antibodies. Finally, down-regulation of MRJP1 and MRJP3 expression via RNAi injection into the brain increased the transition from in-hive nursing to outside foraging, confirming a causal role of these two proteins in the proximate regulation of behavior and life-history of honey bee workers. Interaction partners of MRJP1 and MRJP3 in the honey bee brain included other regulators of honey bee behavior and life history. Thus, our transformative methodological advancement of proteome analysis in honey bees reveals novel regulators of honey bee behavior, extends our understanding of the functional pleiotropy of MRJPs, and supports a general nutrition-based model of the regulation of the age-based division of labor in honey bees.
Elastography of the uterine cervix: implications for success of induction of labor (2011)

Elastography of the uterine cervix may be an objective method for assessment of softening of tissue in the region of the internal os before induction of labor. Standardization of the cervical properties observed on elastography during pregnancy may help to guide the use of prostaglandins or oxytocin for induction of labor.
Excimer Laser Correction of Presbyopia (2007)

The correction of presbyopia with excimer laser surgery on the cornea is the ultimate goal for this type of surgery, since all other treatments for refractive defects have been successfully developed and implemented. Surgery with excimer laser is safe and extremely effective with today’s standards; therefore, most manufacturer companies are working and devoting great research funds and efforts in the development of a technique to treat this aging defect located inside the eye, in the ciliary muscle, and the lens not in the cornea. Several attempts for correcting presbyopia in the cornea with laser surgery have been made. Most of them have not been successful and in fact can be blamed for the bad reputation of surgery on the cornea for the correction of this refractive problem. However, being excimer laser surgery a widely accepted surgery due to its simplicity and safety, this type of surgery has a definitive role in the future treatment of presbyopia. The treatment of presbyopia with excimer laser until a few years ago was based in a technique called monovision. This technique corrects the dominant eye for distant vision and leaves the nondominant eye for near vision with some degree of myopia. Today, however, most laser manufacturers are studying and developing laser ablations to produce multifocality in the cornea. That is the subject of this article.
Phage-based detection of bacterial pathogens (2014)

Bacterial pathogens cause significant morbidity and mortality annually to both humans and animals. With the rampant spread of drug resistance and the diminishing effectiveness of current antibiotics, there is a pressing need for effective diagnostics for detection of bacterial pathogens and their drug resistances. Bacteriophages offer several unique opportunities for bacterial detection. This review highlights the means by which bacteriophages have been utilized to achieve and facilitate specific bacterial detection.
Patterns of Local Failure following Radiation Therapy for Prostate Cancer (2015)

Men with rising prostate specific antigen after radiotherapy for prostate cancer most often experience recurrence in dominant tumor sites. Whether failure is due to inadequate targeting, dosing or intrinsic radiation resistance remains unknown to our knowledge. Further study is warranted.
THERMAL KINETICS of STREPTOCOCCUS FAECIUM IN NUTRIENT BROTH/SOUS VIDE PRODUCTS UNDER PASTEURIZATION CONDITIONS (1995)

There is current major interest in the microbiological aspects and safety of chilled foods such as sous vide. Thermal kinetics for a target microorganism, Streptococcus faecium, was performed and is described in this paper. an E-20 S. faecium was tested for heat resistance in cooked meat nutrient broth. Known cell concentrations were inoculated into ampoules containing the heating medium and exposed to various heating temperatures (60-85C). Swival curves for the recovered S. faecium cells were constructed. the D-values calculated from the logarithm of number of survivors versus time plot were 22.53, 4.47, 1.11, 0.61, 0.29, 0.20 min for 60, 65, 70, 75, 80, 85C, respectively. the z-value obtained from 60–85C was 12.4C; however when only 60–75C was considered, the z-value obtained was 9.4C. Pasteurization values (Pv) calculated for a 13D reduction of S. faecium at 65 and 75C based on the above kinetics and heat penetration data under sous vide processing conditions compared favorably with experimental values in both nutrient broth and in sous vide spaghetti with meat sauce and mackerel with rice products. Using D-values of a heat resistant representative, S. faecium E-20 as a basis, parameters for pasteurization that effectively eliminate vegetative nonspore forming bacteria may be developed. However, the variation in z-values suggest that their usefulness in determining pasteurization process parameters should be carefully considered.
The conserved active-site loop residues of ferrochelatase induce porphyrin conformational changes necessary for catalysis. (2005)

Binding of porphyrin to murine ferrochelatase, the terminal enzyme of the heme biosynthetic pathway, is investigated by employing a set of variants harboring mutations in a putative porphyrin-binding loop. Using resonance Raman (RR) spectroscopy, the structural properties of the ferrochelatase-bound porphyrins are examined, especially with respect to the porphyrin deformation occurring in the environment of the active site. This deformation is thought to be a key step in the enzymatic insertion of ferrous iron into the porphyrin ring to make heme. Our previous RR spectroscopic studies of binding of porphyrin to murine ferrochelatase led us to propose that the wild-type enzyme induces porphyrin distortion even in the absence of the metal ion substrate. Here, we broaden this view by presenting evidence that the degree of a specific nonplanar porphyrin deformation contributes to the catalytic efficiency of ferrochelatase and its variants. The results also suggest that the conserved Trp256 (murine ferrochelatase numbering) is partially responsible for the observed porphyrin deformation. Binding of porphyrin to the ferrochelatase variants causes a decrease in the intensity of RR out-of-plane vibrational mode {gamma}{sub 15}, a saddling-like mode that is strong in the wild-type enzyme. In particular, the variant with a catalytic efficiency 1 order ofmore » magnitude lower than that of the wild-type enzyme is estimated to produce less than 30% of the wild-type saddling deformation. These results suggest that specific conserved loop residues (especially Trp256) are directly involved in the saddling of the porphyrin substrate.« less
Development of Source Testing, Analytical, and Mutagenicity Bioassay Procedures for Evaluating Emissions from Municipal and Hospital Waste Combustors (1992)

Incineration is currently being used for disposal of about 10% of the solid waste generated in the United States, and this percentage will likely increase as land disposal declines. Siting new incinerators, however, is often controversial because of concerns related to the possibility of adverse health effects and environmental contamination from long-term exposure to stack emissions. Specific concerns relate to the adequacies of a) stack emission testing protocols, b) existing regulations, and c) compliance monitoring and enforcement of regulations. U.S. Environmental Protection Agency laboratories are cooperatively conducting research aimed at developing new testing equipment and procedures that will allow a more comprehensive assessment of the complex mixture of organics that is present in stack emissions. These efforts are directed specifically toward developing source testing equipment and procedures, analytical procedures, and bioassay procedures. The objectives of this study were to field test two types of high-volume source dilution samplers, collect stack samples for use in developing analytical and mutagenicity bioassay procedures, and determine mutagenicity of organics associated with emission particles from two municipal waste combustors and a hospital waste combustor. Data are presented for particle concentrations and emission rates, extractable organic concentrations and emission rates, and Salmonella (Ames) mutagenic potency and emission rates. The mutagenic emission rates and emission factors are compared to other incinerators and combustion sources.
A Stable TTI Reverse Time Migration (2011)

We propose a stable TTI acoustic wave equation system by revisiting the anisotropic elastic equations. Based on a VTI system of equations which is equivalent to its elastic counterpart, we introduce self-adjoint differential operators in rotated coordinates to stabilize the TTI acoustic wave equations. Compared with conventional formulations, the new equation system does not add numerical complexity and can be solved by an extremely high order central finite-difference scheme. We show examples that our method provides stable and high quality TTI reverse time migration images.
Modified particle swarm optimization for odor source localization of multi-robot (2011)

Odor source localization is very important in real world applications. We studied the problem of odor source localization and presented a modified particle swarm optimization algorithm for odor source localization of multi robot. The algorithm dynamically adjusts two learning factors in the velocity update equation based on the effect of wind on self cognition and social cognition of a particle. In addition, an artificial potential field method is employed to improve the performance of our algorithm. We conducted various experiments in time-varying environments, and the experimental results confirm the superiority of our algorithm.
Application of fused deposition modelling in controlled drug delivery devices (2007)

Purpose This paper seeks to present an investigation on building controlled drug delivery device (DDD) matrix using fused deposition modelling (FDM) rapid prototyping (RP) process. The focus of the study is on the effect of FDM fabricated macro‐features of reservoir‐matrix DDD models on the drug release rates through the diffusion process. Design/methodology/approach Using various parameters involved with FDM, polymeric DDD matrices with different macro‐features are designed and fabricated on the FDM3000 machine. Experiments are conducted to study the release characteristics and porosity of the fabricated models with a model drug and to see how they are affected by FDM build parameters. Findings Experimental results show that FDM parameters, raster gap and raster angle, play significant roles in controlling the structure and drug release characteristics of the FDM fabricated DDDs. The experimental observations reveal that appropriate FDM parameters can be selected to fabricate controlled DDD device with desired release rate of drug and the desired period of operation of the device. Originality/value The paper introduces a novel application of FDM RP system in the development and fabrication of polymeric controlled DDDs. The controlled release of drugs is an important area in which RP techniques can be successfully used in developing models of release matrix for DDDs with added benefits of accuracy, uniformity and low costs compared with conventional methods.
Adult Stem Cells in Tissue Maintenance and Regeneration (2016)

Adult stem cells, also known as somatic stem cells, reside in specific tissues and possess fundamental properties of stem cells, that is, self-renewal capacity and, though limited in magnitude, multipotency. Generally, these primitive cells are stored in a specialized environment called niche, where they are connected to supporting cells, protected from external harmful stimuli, and kept quiescent until the arrival of an appropriate activating signal. In accordance with the demand of the organ, tissue-specific adult stem cells proliferate, migrate to leave the niche, and differentiate to replace senescent or deteriorated cells, maintaining the organ structure and function. Also, they are known to repair mild injuries in various organs including the skin, liver, intestine, kidney, and bone marrow. Such endogenous regenerative mechanisms, however, appear insufficient to cope with severe damage, as in the case of myocardial infarction [1, 2] or cerebral ischemia [3], in which the damage is mostly irreversible despite the presence of local stem cells. Possibly, tissue-specific biological cues that determine the fate of adult stem cells and their committed progenitors in normal and pathological conditions pose limits to cell differentiation and survival in vivo.
Coronary endarterectomy and stent removal with off-pump coronary artery bypass surgery (2006)

In-stent restenosis remains a significant limitation of coronary artery stenting, occasionally requiring bypass grafting. However, in cases of extensive stent length, the coronary artery-distal graft anastomosis may be technically challenging. We report a patient who underwent implantation of two stents (a proximal 2.5 mm in diameter/24 mm in …
A Brief History of the FFAG Accelerator (2007)

The News Focus article “A half-century late, alternative accelerator takes off” by E. Cartlidge (16 Feb., p. [933][1]) notes the recent revival of the fixed-field alternating-gradient synchrotron (FFAG) accelerator concept, but does not give the history of FFAG. Tihiro Ohkawa in Japan, Keith Symon in the United States, and Andrei Kolomensky in Russia independently invented the FFAG concept. The U.S. group, the Midwest Universities Research Association (MURA), had been formed to develop plans for a high-energy research accelerator program in the Midwest in the early 1950s, and it was within this group that Symon conceived of FFAG and that the three different FFAG electron accelerators were built and operated, studying many aspects of accelerator physics. After MURA learned of Ohkawa's independent invention of FFAG, he was invited to visit the MURA group for the summer of 1955 and then, in 1956, came to the United States to work within MURA for a few years.

 [1]: /lookup/doi/10.1126/science.315.5814.933
The Improvement of the Outcome of Osmotic Demyelination Syndrome by Plasma Exchange (2017)

A 71-year-old Japanese woman presented with progressive fatigue, lethargy, dysarthria and a gait disorder. Her laboratory data revealed hyponatremia (Na 101 mEq/L), and we started correcting her serum sodium level. Within a few days, she became comatose, bedridden, and was intubated. We diagnosed osmotic demyelination syndrome (ODS) and started performing plasma exchange (PE) on the 39th day of hospitalization. She fully recovered after starting PE, and was discharged on foot unassisted. PE can be a beneficial treatment in patients with chronic ODS.
Insulin-Like Growth Factors (IGFs) in Pygmies and Subjects with the Pygmy Trait: Characterization of the Metabolic Actions of IGF I and IGF II in Man* (1982)

Twenty-two pygmy subjects in addition to 11 previously studied pygmies were shown to have low serum concentrations of insulin-like growth factor I (IGF I) and normal serum concentrations of IGF II. Similar findings were noted for the first time in 2 dwarfed adult subjects from the U.S. To determine whether the IGF I deficiency was primary in these patients, we administered human GH (5 mg, twice daily) for 5 days to 11 of the pygmies and the 2 subjects in the U.S. GH-deficient patients and control subjects were studied in a similar manner. At appropriate intervals during treatment, serum urea nitrogen, the serum insulin response to glucose, and, in selected subjects, daily urinary nitrogen, calcium, and phosphate were measured. GH treatment failed to cause a normal increase in IGF I in 9 of 11 pygmy subjects, whereas all GH-deficient subjects had 6–to 10–fold increases in IGF I. GH, likewise, had no effect on IGF I in the 2 subjects from the U.S. with the low IGF I⁄normal IGF II pattern in serum. A significant decrease in the serum urea nitrogen concentration and total urinary nitrogen, a significant increase and a decrease, respectively, in urinary calcium and phosphorus, and significant augmentation of the insulin response to glucose were seen only in subjects with normal or increased IGF I after GH treatment. The combination of normal or increased serum IGF II plus GH given exogenously failed to induce these metabolic changes when IGF I remained low. These data support the hypothesis that a primary deficiency of IGF I is the cause of short staturein the pygmy, and strongly indicate the occurrence of this defect in other ethnic groups. IGF Imay mediate not only the nitrogen-retaining effects of GH, but the insulinotropic and mineralotropic effects as well. (J Clin Endocrinol Metab55:1081, 1982)
Past 50 Years of Influenza Virus Research and It's Future (2003)

Fifty years ago influenza A B and C viruses had al‑ ready been discovered and many of the features including hemagglutination virus neutralization virus replication in ferrets mice and eggs enzyme activity incomplete virus (Von Magnus phenomenon) P ―Q― Rv ariation genetics and reactivation antigenic variation and the swine influ‑ enza lifecycle had been documentated(Hoyle1968) .F owl plague virus of chickens was soon to be recognized as an influenza virus by Shaffer(1955) and interferon was soon to be described by Issacs and Lindenmann(1957) .V ac‑ cines for influenza in humans were still rather crude and were reactogenic in children. Original Antigenic Sin had been described by Francis(1953) .A ntigenic drift in influ‑ enza virus explained the continuous variation in serologi‑ cal reactivity but the occasional major changes that oc‑ curred with the emergence of new pandemic strains like Asian/H2N2/195 7o r Hon gK ong/H3N2/196 8w ere unexplained. In the past50years influenza virus has served as a su‑ perb model system for the study of the replication genet‑ ics immunology and structure of segmented RNA viruses. By necessity I will focus only on a limited number of areas including Original Antigenic Sin the ecology of influenza Av irusesand their global distribution in aquatic birds ge‑ netic drift and shift and the emergence and pathogenesis of influenza viruses in animal models. Recent studies using reverse genetics have established that the NS1gene of the A/Hong Kong/156/97(H5N1)influenza virus can counteract host cell cytokine activity and that pigs in‑ fected with constructs containing this gene were severely ill. The future is extremely exciting for influenza viruses can now really bemade to orderand the genomics of both the virus and the host are at hand. Influenza is a truly global problem and there is still a paucity of information on influenza genomics. Through continuing international col‑ laborations this information will be obtained and we will define both the viral and host factors that permit influenza viruses to transmit between species and may then be able to predict pandemic potential. During this process we must be cognizant that influenza has continuing potential to be a man made or natural bioterrorism agent and that new strategies to control influenza are urgently needed in‑ cluding stockpiling of antiviral drugs.
Enhance up to 40% performance of SH-4A processor by using Prefix instruction (2010)

Instruction set development is an effective way to improve processor performance. In SH-4A core enhancement, Prefix instruction is introduced as a technique to enrich function of original instruction. As a result, we have successfully integrated 130 new 32-bit instructions to 16-bit original instruction set and performance of new core is improved up to 43% compared to conventional model.
Image Reconstruction from Phase Information Only (1970)

A quantitative analysis of the effect on image reconstruction of discarding the amplitude information contained in a wavefront reflected by a diffusely reflecting, coherently illuminated surface is given. The image reconstruction from a phase record alone is analyzed for the perfect and imperfect phase-matching cases.