gebhart/patrepeval huggingface dataset:
Medicine, religion and the puritan revolution (1989)

The first major critique of orthodox medical practice in England was composed as early as 1585 by the Paracelsian, Richard Bostocke, yet no attempt to implement a programme of medical reform took place until the 1650s – the years of the so-called ‘puritan revolution’. Not surprisingly, many historians have for some time assumed that the well-documented opposition to medical orthodoxy in the middle decades of the seventeenth century must have been related to some extent to the political and religious upheavals of these years. In particular, it has become widely accepted that the beliefs and values associated with the puritan movement were largely responsible for the promotion of reform, not just in medicine and natural science, but in all aspects of early modern English society. In the words of R.F. Jones, ‘the Puritans were out to reform not only Church and State in their narrow connotations, but almost everything else’.
Learning small-size DNN with output-distribution-based criteria (2014)

Deep neural network (DNN) obtains significant accuracy improvements on many speech recognition tasks and its power comes from the deep and wide network structure with a very large number of parameters. It becomes challenging when we deploy DNN on devices which have limited computational and storage resources. The common practice is to train a DNN with a small number of hidden nodes and a small senone set using the standard training process, leading to significant accuracy loss. In this study, we propose to better address these issues by utilizing the DNN output distribution. To learn a DNN with small number of hidden nodes, we minimize the Kullback–Leibler divergence between the output distributions of the small-size DNN and a standard large-size DNN by utilizing a large number of un-transcribed data. For better senone set generation, we cluster the senones in the large set into a small one by directly relating the clustering process to DNN parameters, as opposed to decoupling the senone generation and DNN training process in the standard training. Evaluated on a short message dictation task, the proposed two methods get 5.08% and 1.33% relative word error rate reduction from the standard training method, respectively.
Safety, Tolerability, and Clinical Response After Fecal Transplantation in Children and Young Adults With Ulcerative Colitis (2013)

Fecal enemas were feasible and tolerated by children with UC. Adverse events were acceptable, self-limiting, and manageable by subjects. FMT indicated efficacy in the treatment of UC.
Improved isolation strategies to increase the yield and purity of human urinary exosomes for biomarker discovery (2018)

Circulating miRNAs are detected in extracellular space and body fluids such as urine. Circulating RNAs can be packaged in secreted urinary extracellular vesicles (uEVs) and thus protected from degradation. Urinary exosome preparations might contain specific miRNAs, relevant as biomarkers in renal and bladder diseases. Major difficulties in application of uEVs into the clinical environment are the high variability and low reproducibility of uEV isolation methods. Here we used five different methods to isolate uEVs and compared the size distribution, morphology, yield, presence of exosomal protein markers and RNA content of uEVs. We present an optimized ultracentrifugation and size exclusion chromatography approach for highly reproducible isolation for 50-150 nm uEVs, corresponding to the exosomes, from 50 ml urine. We profiled the miRNA content of uEVs and total urine from the same samples with the NanoString platform and validated the data using qPCR. Our results indicate that 18 miRNAs, robustly detected in uEVs were always present in the total urine. However, 15 miRNAs could be detected only in the total urine preparations and might represent naked circulating miRNA species. This is a novel unbiased and reproducible strategy for uEVs isolation, content normalization and miRNA cargo analysis, suitable for biomarker discovery studies.
Predictive In Vitro Models of the Sterilizing Activity of Anti-Tuberculosis Drugs (2004)

Sterilizing drugs kill Mycobacterium tuberculosis that persists during chemotherapy. Predictive models should mimic the conditions causing persistence in the lesions of cavitary disease, and should grade current anti-tuberculosis drugs according to their sterilizing activity determined in clinical trials. Models should start with old, stationary cultures grown micro-aerophilically. In these, persistent bacilli occur in different populations in which there is no appreciable cell division. Population 1. Grows in liquid culture medium but not on solid medium. Killed by rifampicin. Population 2. Grows on solid culture medium. Killed by rifampicin. Population 3. Grows in liquid medium but not on solid medium. Tolerant of rifampicin. Population 4. Bacilli from Cornell model mice, after treatment with pyrazinamide and isoniazid, cannot grow in liquid or on solid culture medium. Some of these populations are incorporated in models which start with 100-day liquid medium cultures. In model 1 (population 2) the new drug is added and colony counted after 7 days incubation. In models 2 and 3, 100 mg/L rifampicin is added to the 100-day culture when the bacilli lose their ability to grow on solid culture medium (population 3). After re-suspension in rifampicin-free liquid medium for 7 days, the bacilli recover growth on solid medium, when a colony count is done. The new drug is added during incubation with rifampicin in model 3 and at the start of recovery in drug-free medium in model 2. Models 1 and 3 grade isoniazid, rifampicin and pyrazinamide according to their sterilizing activity determined by clinical trials.
Chlamydia pneumoniae Expresses Genes Required for DNA Replication but Not Cytokinesis during Persistent Infection of HEp-2 Cells (2001)

Chlamydia pneumoniae causes community-acquired pneumonia and is associated with several chronic diseases, including asthma and atherosclerosis. The intracellular growth rate of C. pneumoniae slows dramatically during chronic infection, and such persistence leads to attenuated production of new elementary bodies, appearance of morphologically aberrant reticulate bodies, and altered expression of several chlamydial genes. We used an in vitro system to further characterize persistent C. pneumoniae infection, employing both ultrastructural and transcriptional activity measurements. HEp-2 cells were infected with C. pneumoniae (TW-183) at a multiplicity of infection of 3:1, and at 2 h postinfection gamma interferon (IFN-gamma) was added to the medium at 0.15 or 0.50 ng/ml. Treated and untreated cultures were harvested at several times postinfection. RNA was isolated and reverse transcribed, and reverse transcription (RT)-PCR analyses targeting primary transcripts from chlamydial rRNA operons as well as dnaA, polA, mutS, minD, ftsK, and ftsW mRNA were done. Some cultures were fixed and stained for electron microscopic analysis, and a real-time PCR assay was used to assess relative chlamydial chromosome accumulation under each culture condition. The latter assays showed that bacterial chromosome copies accumulated severalfold during IFN-gamma treatment of infected HEp-2 cells, although less accumulation was observed in cells treated with the higher dose. Electron microscopy demonstrated that high-dose IFN-gamma treatment elicited aberrant forms of the bacterium. RT-PCR showed that chlamydial primary rRNA transcripts were present in all IFN-gamma-treated and untreated cell cultures, indicating bacterial metabolic activity. Transcripts from dnaA, polA, mutS, and minD, all of which encode products for bacterial chromosome replication and partition, were expressed in IFN-gamma-treated and untreated cells. In contrast, ftsK and ftsW, encoding products for bacterial cell division, were expressed in untreated cells, but expression was attenuated in cells treated with low-dose IFN-gamma and absent in cells given the high dose of cytokine. Thus, the development of persistence included production of transcripts for DNA replication-related, but not cell division-related, genes. These results provide new insight regarding molecular activities that accompany persistence of C. pneumoniae, as well as suggesting requirements for reactivation from persistent to productive growth.
Predicting protein crystallization from a dilute solution property (1994)

A dilute solution parameter obtained from static light-scattering measurements is proposed as a predictor for protein crystallization experiments. The osmotic second virial coefficients, B(22), have been measured for a variety of proteins in solvents that are known to promote crystallization and the values for B(22) were found to lie within a fairly narrow range which we refer to as a crystallization slot. Solution conditions which were known not to favor crystallization of the proteins resulted in B(22) values well outside the crystallization slot.
The FLP recombinase of the yeast 2-micron plasmid: characterization of its recombination site. (1985)

The minimal size of the recombination site required for efficient FLP recombinase-catalyzed recombination in vitro is no more than 28 base pairs, which includes parts of two 13-base-pair inverted repeats and all of an 8-base-pair spacer. The FLP recombinase cleaves the DNA at the boundaries of the spacer, becomes covalently linked to the spacer DNA via a 3' phosphate, and leaves a free 5' hydroxyl at the other end of the 8-base-pair spacer. The efficiency of recombination is reduced if the size of the spacer in a recombinant site is increased or decreased by 1 base pair, while the spacer in the second site is unaltered. Recombination between two sites with identical 1-base-pair additions or deletions in the spacer, however, is relatively unaffected. This result suggests that pairing of sequences in the spacer region is important in FLP-promoted recombination events. The sequence asymmetry utilized by the recombinase to determine the orientation of the site is located uniquely within the spacer region.
<title>Adaptive source rate control for wireless video conferencing</title> (1997)

Hybrid ARQ schemes can yield much better throughput and reliability than static FEC schemes for the transmission of data over time-varying wireless channels. However these schemes result in higher delay. They adapt to the varying channel conditions by retransmitting erroneous packets, this results in variable effective data rates for current PCS networks because the channel bandwidth is constant. Hybrid ARQ schemes are currently being proposed as the error control schemes for real-time video transmission. The standardization process is on-going in ITU, MPEG-4 and wireless ATM forum. The important issue is how to ensure low delay while taking advantage of the high throughput and reliability that these schemes provide for. In this paper we propose an adaptive source rate control (ASRC) protocol which can work together with the hybrid ARQ error control schemes to achieve efficient transmission of real-time video with low delay and high reliability. The ASRC scheme adjusts the source rate based on the channel conditions, the transport buffer occupancy and the delay constraints. It optimizes the video quality by dynamically changing both the number of the forced update (intracoded) macroblocks and the quantization scale used in a frame. The number of the forced update macroblocks used in a frame is first adjusted according to the allocated source rate. This reduces the fluctuation of the quantization scale with the change in the channel conditions during encoding so that the uniformity of the video quality is improved. The simulation results show that the proposed ASRC protocol performs very well for both slow fading and fast fading channels.
露天开采：技术述评（一） (2002)

综合评述了2001年世界上露天矿用钻机、挖掘机、汽车以及相关高新技术的进展情势与特点；重点列述了各主要设备制造公司近年推出的新型产品。作者指出：设备大型化势头不减；自动化水平不断上升；各种高新科技手段，尤其是信息技术使露天矿生产效率明显提高。
Cyberpunc: a lightweight punctuation annotation system for speech (2002)

This paper describes a lightweight method for the automatic insertion of intra-sentence punctuation into text. Despite the intuition that pauses in an acoustic stream are a positive indicator for some types of punctuation, this work will demonstrate the feasibility of a system which relies solely on lexical information. Besides its potential role in a speech recognition system, such a system could serve equally well in non-speech applications such as automatic grammar correction in a word processor and parsing of spoken text. After describing the design of a punctuation-restoration system, which relies on a trigram language model and a straightforward application of the Viterbi algorithm, we summarize results, both quantitative and subjective, of the performance and behavior of a prototype system.
Membrane proteins PmpG and PmpH are major constituents of Chlamydia trachomatis L2 outer membrane complex (2000)

The outer membrane complex of Chlamydia is involved in the initial adherence and ingestion of Chlamydia by the host cell. In order to identify novel proteins in the outer membrane of Chlamydia trachomatis L2, proteins were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. By silver staining of the protein profile, a major protein doublet of 100-110 kDa was detected. In-gel tryptic digestion and matrix-assisted laser desorption/ionization mass spectrometry identified these proteins as the putative outer membrane proteins PmpG and PmpH.
Added Value of a Serum Proteomic Signature in the Diagnostic Evaluation of Lung Nodules (2012)

This study suggests a possible role of a blood biomarker in the evaluation of indeterminate lung nodules.
Antineoplastic agents. Structure-activity relationship study of bis(substituted aminoalkylamino)anthraquinones (1978)

A structure-activity relationship study was conducted on a number of bis(substituted aminoalkylamino)anthraquinones. These compounds were prepared by the condensation of substituted or unsubstituted leucoquinizarin with appropriate amines, followed by air oxidation. Both the position and the nature of the center nitrogen atom of the side chain are vital to the antineoplastic activity. The possible mode of action of these aminoquinones was discussed. 1,4-Dihydroxy-5,8-bis[[2-(hydroxyethyl)amino]ethyl]amino-9,10-anthracenedione (DHAQ) was found to possess potent inhibitory activity against both the P-388 leukemia system (T/C of 299 at 0.5 mg/kg with 4/6 cures) and the B-16 melanoma system (T/C of 503 at 1 mg/kg with 7/10 cures).
The overactive bladder (2010)

Urinary urgency and the associated symptoms which comprise overactive bladder are prevalent amongst the general population and adversely affect quality of life. Disease management consists of a sequential series of options starting with behavioural and lifestyle techniques, pharmacological management (antimuscarinics) and, in severe cases, surgical treatment (urinary diversion, neuromodulation, augmentation cystoplasty and detrusor myectomy). There is increasing recognition of pathophysiological mechanisms in the urothelium, interstitial cells and afferent neurons allowing the importance of peripheral integrative interaction to be identified. The hierarchy of the central nervous system control adds additional complexity to understanding the oflower urinary tract function. Some newer methods of treatment include Botulinum toxin A intramural injections, oral beta-3 adrenergic agonists and rho-kinase inhibitors. The lack of a disease generating hypothesis, the lack of animal models for disease and the subjective nature of the central symptom (urgency) still pose considerable theoretical and scientific hurdles that need to be overcome in the treatment of this condition.
Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. (1996)

The pivotal role of G proteins in sensory, hormonal, inflammatory, and proliferative responses has provoked intense interest in understanding how they interact with their receptors and effectors. Nonetheless, the locations of the receptors and effector binding sites remain poorly characterized, although nearly complete structures of the alphabetagamma heterotrimeric complex are available. Here we apply evolutionary trace (ET) analysis [Lichtarge, O., Bourne, H. R. & Cohen, F. E. (1996) J. Mol. Biol. 257, 342-358] to propose plausible locations for these sites. On each subunit, ET identifies evolutionarily selected surfaces composed of residues that do not vary within functional subgroups and that form spatial clusters. Four clusters correctly identify subunit interfaces, and additional clusters on Galpha point to likely receptor or effector binding sites. Our results implicate the conformationally variable region of Galpha in an effector binding role. Furthermore the range of predicted interactions between the receptor and Galphabetagamma, is sufficiently limited that we can build a low resolution and testable model of the receptor-G protein complex.
The Potential of PARP Inhibitors in Neuro-Oncology (2012)

DNA damaging agents have an integral role in the treatment of brain tumors. Recent advances in our understanding of how cancer cells repair DNA damage have made it possible to consider modification of the DNA damage response as a way in which resistance to radiotherapy and chemotherapy might be overcome. PARP inhibitors are potent but nontoxic drugs that inhibit repair of DNA single-strand breaks and increase the cytotoxic effects of radiotherapy and alkylating chemotherapy agents, including temozolomide. PARP inhibitors have potential applications in neuro-oncology because there is increasing evidence that their radio- and chemo-sensitizing effects are tumor specific. This review explores the mechanisms of action of PARP inhibitors and describes their putative mechanisms of radio- and chemo-sensitization in the context of CNS oncology. The authors go on to review their development in recent clinical trials, with a focus on glioblastoma.
Immunocytochemical localization of granulin-1 to mononuclear phagocytic cells of the teleost fish Cyprinus carpio and Carassius auratus (1995)

A new class of low-molecular-weight cysteine-rich regulatory growth factors, designated granulins, has been isolated from hematopoietic tissues of a teleost fish (Cyprinus carpio) and structurally characterized. Granulin-1, the predominant form found in carp spleen, was used to raise polyclonal antibodies in rabbits and to establish a radioimmunoassay. This permitted preliminary tissue distribution studies of granulin-1 to be undertaken in carp (Cyprinus carpio) and goldfish (Carassius auratus). Granulin-1 immunoreactivity was found in the melanomacrophage centers of the spleen and head kidney. Carp tissues anatomically involved in the first line of defense against infection, including skin, gills, gut, and also heart, showed intense granulin-1 immunoreactive staining within presumptive macrophage cells. Granulin-1 immunoreactive macrophages prepared from goldfish spleen and head kidney adhered to glass slides, actively phagocytosed carbon particles, and contained granulin-1 immunoreactivity as well as abundant endogenous peroxidase activity. This study demonstrates that granulin-1 is synthesized and stored in macrophages/monocytes of spleen, head kidney, and peripheral tissues of teleost fish.
Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum (2008)

Schizophrenia (SCZ) is a common, disabling mental illness with high heritability but complex, poorly understood genetic etiology. As the first phase of a genomic convergence analysis of SCZ, we generated 16.7 billion nucleotides of short read, shotgun sequences of cDNA from post-mortem cerebellar cortices of 14 patients and six, matched controls. A rigorous analysis pipeline was developed for analysis of digital gene expression studies. Sequences aligned to approximately 33,200 transcripts in each sample, with average coverage of 450 reads per gene. Following adjustments for confounding clinical, sample and experimental sources of variation, 215 genes differed significantly in expression between cases and controls. Golgi apparatus, vesicular transport, membrane association, Zinc binding and regulation of transcription were over-represented among differentially expressed genes. Twenty three genes with altered expression and involvement in presynaptic vesicular transport, Golgi function and GABAergic neurotransmission define a unifying molecular hypothesis for dysfunction in cerebellar cortex in SCZ.
Remote point-of-gaze estimation requiring a single-point calibration for applications with infants (2008)

This paper describes a method for remote, non-contact point-of-gaze estimation that tolerates free head movements and requires a simple calibration procedure in which the subject has to fixate only on a single point. This method uses the centers of the pupil and at least two corneal reflections that are estimated from eye images captured by at least two cameras. Experimental results obtained with three adult subjects exhibited RMS point-of-gaze estimation errors ranging from 7 to 12 mm (equivalent to about 0.6 -- 1° of visual angle) for head movements in a volume of about 1 dm3. Preliminary results with two infants demonstrated the ability of a system that requires a single-point calibration procedure to estimate infants' point-of-gaze. The ability to record infants' visual scanning behavior can be used for the study of visual development, the determination of attention allocation and the assessment of visual function in preverbal infants.
Computing nearest-neighbor fields via Propagation-Assisted KD-Trees (2012)

Matching patches between two images, also known as computing nearest-neighbor fields, has been proven a useful technique in various computer vision/graphics algorithms. But this is a computationally challenging nearest-neighbor search task, because both the query set and the candidate set are of image size. In this paper, we propose Propagation-Assisted KD-Trees to quickly compute an approximate solution. We develop a novel propagation search method for kd-trees. In this method the tree nodes checked by each query are propagated from the nearby queries. This method not only avoids the time-consuming backtracking in traditional tree methods, but is more accurate. Experiments on public data show that our method is 10-20 times faster than the PatchMatch method [4] at the same accuracy, or reduces its error by 70% at the same running time. Our method is also 2-5 times faster and is more accurate than Coherency Sensitive Hashing [22], a latest state-of-the-art method.
Optimizing cuff width for noninvasive measurement of blood pressure (2000)

The optimum cuff width for the indirect measurement of blood pressure is not directly proportional to arm circumference, but is proportional to the logarithm of the arm's circumference.
Image-sharpness criterion for space-variant imaging (1981)

Image-sharpness criteria studied previously have depended on the assumption of the spatial stationarity of the point-spread function of the degrading medium plus the imaging lens system. If this assumption does not hold, the sharpness criteria no longer necessarily reach their extrema when system aberrations are zero. A criterion has been constructed that avoids this dependency, although at the expense of requiring information that is unnecessary in the spatially stationary case. After the instantaneous degraded image is filtered with a transfer function that is equal to or slightly greater than the transfer function of the degrading medium, the resulting image must be equal to the long-term-averaged image. The instantaneous image before modification is therefore diffraction limited or almost diffraction limited. The criterion may be applied locally.