gebhart/patrepeval huggingface dataset:
Latent Predictor Networks for Code Generation (2016)

Many language generation tasks require the production of text conditioned on both structured and unstructured inputs. We present a novel neural network architecture which generates an output sequence conditioned on an arbitrary number of input functions. Crucially, our approach allows both the choice of conditioning context and the granularity of generation, for example characters or tokens, to be marginalised, thus permitting scalable and effective training. Using this framework, we address the problem of generating programming code from a mixed natural language and structured specification. We create two new data sets for this paradigm derived from the collectible trading card games Magic the Gathering and Hearthstone. On these, and a third preexisting corpus, we demonstrate that marginalising multiple predictors allows our model to outperform strong benchmarks.
Differential Expression of Oestrogen Regulated Genes in Breast Cancer (1995)

Pathological endpoints such as tumour size, lymph node status and vascular invasion remain the most useful guides in selecting treatment strategies for breast cancer. There is a need, however, to further investigate the molecular mechanisms that determine the properties of an individual tumour e.g., hormone responsiveness and probability of metastasis. While numerous prognostic factors have now been identified few have contributed to defining clinical response to therapy. Oestrogen-regulated genes are likely to be important since they not only define a functional oestrogen receptor, but alterations in their expression might provide insights into the mechanisms involved in tumour progression and loss of endocrine sensitivity. Recently an oestrogen responsive gene, pLIV1, has been isolated and shown to be expressed in ER+ disease where it appears to predict nodal involvement. The present paper describes aspects of its regulation and discusses the potential role of this and other genes in the development of endocrine resistance.
Development of Liposomal Ciprofloxacin to Treat Lung Infections (2016)

Except for management of Pseudomonas aeruginosa (PA) in cystic fibrosis, there are no approved inhaled antibiotic treatments for any other diseases or for infections from other pathogenic microorganisms such as tuberculosis, non-tuberculous mycobacteria, fungal infections or potential inhaled biowarfare agents including Francisella tularensis, Yersinia pestis and Coxiella burnetii (which cause pneumonic tularemia, plague and Q fever, respectively). Delivery of an antibiotic formulation via the inhalation route has the potential to provide high concentrations at the site of infection with reduced systemic exposure to limit side effects. A liposomal formulation may improve tolerability, increase compliance by reducing the dosing frequency, and enhance penetration of biofilms and treatment of intracellular infections. Two liposomal ciprofloxacin formulations (Lipoquin(®) and Pulmaquin(®)) that are in development by Aradigm Corporation are described here.
[Experimental study of acute spinal cord injury: a histopathological study]. (1993)

The microscopic appearance of a rat spinal cord which was acutely compressed by aneurysmal clip for one minute, was investigated 15 minutes, 30 minutes, 1 hour, 3 hours and 6 hours after the injury. Although the resulting small hemorrhagic lesion involved primarily only the central gray matter of the injured portion 15 minutes after compression injury, hemorrhage, necrosis and edema in the central gray matter enlarged progressively until 3 hours after injury. Petechial hemorrhage, necrosis and edema were observed in the surrounding area one hour after spinal compression. Then these pathological changes extended rostrally and caudally, but their extension was more significantly remarkable in the rostral side than in the caudal side 3 hours after compression. It was observed that leukocytes begin to infiltrate into the injured capillary walls and plug up the capillary lumen 30 minutes after the injury. Three hours following the injury, leukocytes (lymphocyte, macrophage) extravasated into the surrounding spinal tissue. From these histopathological observations, we reached the following conclusions. A. Secondary injuries play an important role in grave impairment of neurological function of the spinal cord following acute trauma. B. Pathological findings (hemorrhage necrosis and edema) extend more prominently to the rostral side, because the direction of spinal blood flow may be rostral in the thoracic spinal cord. C. Severe disturbance of intraspinal capillary blood flow leading to grave spinal damage may be evoked, because leukocytes infiltrate into the capillary around the injured area and plug up the their lumen about 30 minutes after the injury.
Assessment of Knee Cartilage in Cadavers with Dual-Detector Spiral CT Arthrography and MR Imaging (2002)

Dual-detector spiral CT arthrography of the knee is a valuable method for the assessment of open cartilage lesions of the entire knee.
Monocyte-mediated augmentation of human natural killer cell activity: conditions, monocyte and effector cell characteristics. (1986)

The characteristics of the effector cells and monocytes, and conditions required for the monocyte-mediated augmentation of human natural killer (NK) cell activity were investigated. Enriched null cell populations were further fractionated by Percoll centrifugation and used as effector cells. The LGL-enriched fraction was less susceptible than either the unfractionated cells or the other Percoll fractions to the monocyte augmentation when mixed with monocytes in the chromium-release assay and when precultured with monocytes for 12 hr, retrieved by carbonyl iron treatment, and tested for NK activity against K562. This differential susceptibility was reflected at the single cell level. The LGL-enriched Percoll fraction did not display the increase in target-binding cells with lytic activity that was exhibited by the other effector cell preparations after culture with monocytes. No differences in Leu-7 and Leu-11 phenotypes were detected between enriched null cells that had been cultured with and without monocytes for 12 hr. At the monocyte level, it was shown that pretreatment of the monocytes with LPS did not alter their NK-augmenting activity appreciably. Glutaraldehyde-fixed monocytes were not effective, and actinomycin D-treated monocytes were less effective than untreated or irradiated monocytes when mixed with enriched null cells in the assay. Actinomycin D-treated monocytes did not augment and possibly suppressed NK activity tested after 12-hr culture, and irradiated monocytes were less effective for augmenting NK activity than untreated cells. Monocyte-mediated augmentation could be detected when the medium used for null cell-monocyte coculture was supplemented with a) different lots of fetal bovine serum, b) human AB serum, c) autologous serum, or d) no serum. Polymyxin B and indomethacin did not alter the monocyte effect. Finally, the monocyte-mediated augmentation of human NK was not MHC restricted, since allogeneic combinations were also effective. These results suggest that 1) lymphocytes other than LGL participate in the monocyte-mediated augmentation of NK activity, 2) the augmentation is probably activational rather than maturational, 3) the monocytes must be viable to be effective when mixed with null cells during the assay, 4) de novo RNA and/or protein synthesis by the monocytes is required for the monocytes to induce augmented activity in null cells after 12-hr coculture, 5) prostaglandin synthesis and endotoxin are probably not involved in the augmentation, 6) the phenomenon is not MHC restricted, and 7) monocytes may express augmentative and suppressive activities concurrently.
Bidirectional Multirate Reconstruction for Temporal Modeling in Videos (2017)

Despite the recent success of neural networks in image feature learning, a major problem in the video domain is the lack of sufficient labeled data for learning to model temporal information. In this paper, we propose an unsupervised temporal modeling method that learns from untrimmed videos. The speed of motion varies constantly, e.g., a man may run quickly or slowly. We therefore train a Multirate Visual Recurrent Model (MVRM) by encoding frames of a clip with different intervals. This learning process makes the learned model more capable of dealing with motion speed variance. Given a clip sampled from a video, we use its past and future neighboring clips as the temporal context, and reconstruct the two temporal transitions, i.e., present-past transition and present-future transition, reflecting the temporal information in different views. The proposed method exploits the two transitions simultaneously by incorporating a bidirectional reconstruction which consists of a backward reconstruction and a forward reconstruction. We apply the proposed method to two challenging video tasks, i.e., complex event detection and video captioning, in which it achieves state-of-the-art performance. Notably, our method generates the best single feature for event detection with a relative improvement of 10.4% on the MEDTest-13 dataset and achieves the best performance in video captioning across all evaluation metrics on the YouTube2Text dataset.
Simulated Biological Fluids with Possible Application in Dissolution Testing (2011)

This literature review is a compilation of the composition and, in most cases, the preparation instructions for simulated biological fluids that may be used as dissolution media in the evaluation of dissolution profiles and amount of drug released from pharmaceutical dosage forms. The use of simulated biological fluids can give a better understanding of the release mechanisms and possible in vivo behavior of a product and enhance the predictive capability of the dissolution testing. A summary of the major characteristics of the most used routes of administration that may affect dissolution and absorption of drug substances is presented. The routes and simulated biological fluids covered by this review are:
Neutralizing Tumor-Promoting Chronic Inflammation: A Magic Bullet? (2013)

There have been substantial advances in cancer diagnostics and therapies in the past decade. Besides chemotherapeutic agents and radiation therapy, approaches now include targeting cancer cell-intrinsic mediators linked to genetic aberrations in cancer cells, in addition to cancer cell-extrinsic pathways, especially those regulating vascular programming of solid tumors. More recently, immunotherapeutics have entered the clinic largely on the basis of the recognition that several immune cell subsets, when chronically activated, foster tumor development. Here, we discuss clinical and experimental studies delineating protumorigenic roles for immune cell subsets that are players in cancer-associated inflammation. Some of these cells can be targeted to reprogram their function, leading to resolution, or at least neutralization, of cancer-promoting chronic inflammation, thereby facilitating cancer rejection.
Add-back therapy with GnRH analogues for uterine fibroids (2015)

There was low or moderate quality evidence that tibolone, raloxifene, estriol and ipriflavone help to preserve bone density and that MPA and tibolone may reduce vasomotor symptoms. Larger uterine volume was an adverse effect associated with some add-back therapies (MPA, tibolone and conjugated estrogens). For other comparisons, outcomes of interest were not reported or study findings were inconclusive.
Antiviral and Antiproliferative Effects of Interferons Delivered via Monoclonal Antibodies (1984)

We present in vitro experiments demonstrating the feasibility of specifically targeting IFNs by coupling to monoclonal antibodies (MAbs). Human interferon alpha (HuIFN-alpha), both natural and recombinant, were coupled to Epstein-Barr virus (EBV) membrane antigen (MA) specific MAbs and shown to retain full antiviral and antiproliferative activities when tested on several human cell lines. A series of in vitro pulsing experiments demonstrated that a minimum amount of MAb-delivered IFN exerts pronounced antiviral and antiproliferative effects on human QIMR-WIL target cells which carry EBV (viral) membrane antigens (EBV-MA+) and not on U-266 or Hep2 cell lines (EBV-MA-). Additionally the antiproliferative action of MAb-coupled rIFN-alpha appeared to be enhanced compared with that of uncoupled.
Rapid ocular angiogenic control via naked DNA delivery to cornea. (2001)

The cornea is readily accessible for gene therapy in the laboratory and in the clinic. The method described is safe, effective, titratable, and easily monitored. Naked DNA delivery to the cornea has the potential to alter the treatment of a wide variety of corneal and anterior segment diseases.
Fluoxetine improves emotional incontinence (1992)

Emotional incontinence is a behavioural syndrome characterized by involuntary weeping, grimacing, and/or laughter. We investigated the efficacy of fluoxetine in 13 patients with emotional incontinence. All 13 patients demonstrated dramatic improvement in emotional lability within 3 to 14 days.
Identification and characterization of fully human anti-CD22 monoclonal antibodies (2009)

CD22 is a member of the B cell receptor family and is implicated in B cell function and development. It is expressed on multiple forms of B cell lymphoma and is an attractive cancer therapeutic target. We report here the identification of two fully human anti-CD22 antibodies using phage display methodology. Both antibodies exhibit specific binding to cell surface-associated CD22 in multiple B cell lines. Through ELISA using mammalian cell-expressed sub-domains of CD22 as binding antigen, we mapped the binding epitopes of the newly identified CD22 antibodies to be within the Ig-like domains 5 to 7 of CD22. Their epitopes do not overlap with those of several therapeutic antibodies currently in preclinical or clinical development. These antibodies have potential as cancer therapeutic candidates and research reagents.
Magnetocaloric effect in epitaxial La0.56Sr0.44MnO3 alloy and digital heterostructures (2012)

This work investigates the magnetocaloric effect of two epitaxial manganite heterostructures, one being a single layer La0.56Sr0.44MnO3 alloy with randomly distributed La and Sr cations, the other a digitally synthesized superlattice of LaMnO3 and SrMnO3 fabricated to be compositionally identical to the alloy. The magnetic entropy change and relative cooling power were larger for the alloy than the superlattice, though both are suppressed relative to bulk materials. These results indicate that disorder of the A-site cation species in the perovskite structure may play a crucial role in defining the magnetocaloric effect in complex oxide materials.
Multiplexed expression and screening for recombinant protein production in mammalian cells (2006)

The combination of small scale multi-well plate culture and dot blotting described here will allow the multiplex analysis of different mammalian expression experiments enabling a faster identification of high yield expression constructs or conditions prior to large scale protein production. The methods for parallel GATEWAY cloning and expression of multiple constructs in cell culture will also be useful for applications such as the generation of receptor protein microarrays.
Statistical inference for ordinary differential equations using gradient matching (2017)

A central objective of current systems biology research is explaining the interactions amongst components in biopathways. A standard approach is to view a biopathway as a network of biochemical reactions, which is modelled as a system of ordinary differential equations (ODEs).

Conventional inference methods typically rely on searching the space of parameter values, and at each candidate, numerically solving the ODEs and comparing the output with that observed. After choosing an appropriate noise model, the form of the likelihood is defined, and a measure of similarity between the data signals and the signals described by the current set of ODE parameters can be calculated. This process is repeated, as part of either an iterative optimisation scheme or sampling procedure in order to estimate the parameters. However, the computational costs involved with repeatedly numerically solving the ODEs are usually high.

Several authors have adopted approaches based on gradient matching, aiming to reduce this computational complexity. These approaches are based on the following two-step procedure. At the first step, interpolation is used to smooth the time series data, in order to avoid modelling noisy observations; in a second step, the kinetic parameters of the ODEs are either optimised or sampled, whilst minimising some metric measuring the difference between the slopes of the tangents to the interpolants, and the parameter-dependent time derivative from the ODEs. In this fashion, the ODEs never have to be numerically integrated, and the problem of inferring the typically unknown initial conditions of the system is removed, as it is not required for matching gradients. A downside to this two-step scheme is that the results of parameter inference are critically dependent on the quality of the initial interpolant. Alternatively, the ODEs can be allowed to regularise the interpolant and it has been demonstrated that it significantly improves the parameter inference accuracy and robustness with respect to noise.

This thesis extends and develops methods of gradient matching for parameter inference and model selection in ODE systems in a systems biology context.
Cloning of cDNA encoding the bifunctional dehydroquinase.shikimate dehydrogenase of aromatic-amino-acid biosynthesis in Nicotiana tabacum (1994)

Nicotiana tabacum cDNA encoding a bifunctional protein having catalytic domains for dehydroquinase and shikimate dehydrogenase was cloned and sequenced. Complementation of Escherichia coli aroD and aroE auxotrophs was successful. Amino acid sequencing located the N-terminus of the mature protein. The two catalytic domains exhibited greater amino acid identity with prokaryote homologues than with yeast and fungal homologues.
Transduction Efficiency and Immune Response Associated With the Administration of AAV8 Vector Into Dog Skeletal Muscle (2008)

Recombinant adeno-associated virus (rAAV)-mediated gene transfer is an attractive approach to the treatment of Duchenne muscular dystrophy (DMD). We investigated the muscle transduction profiles and immune responses associated with the administration of rAAV2 and rAAV8 in normal and canine X-linked muscular dystrophy in Japan (CXMD(J)) dogs. rAAV2 or rAAV8 encoding the lacZ gene was injected into the skeletal muscles of normal dogs. Two weeks after the injection, we detected a larger number of beta-galactosidase-positive fibers in rAAV8-transduced canine skeletal muscle than in rAAV2-transduced muscle. Although immunohistochemical analysis using anti-CD4 and anti-CD8 antibodies revealed less T-cell response to rAAV8 than to rAAV2, beta-galactosidase expression in rAAV8-injected muscle lasted for <4 weeks with intramuscular transduction. Canine bone marrow-derived dendritic cells (DCs) were activated by both rAAV2 and rAAV8, implying that innate immunity might be involved in both cases. Intravenous administration of rAAV8-lacZ into the hind limb in normal dogs and rAAV8-microdystrophin into the hind limb in CXMD(J) dogs resulted in improved transgene expression in the skeletal muscles lasting over a period of 8 weeks, but with a declining trend. The limb perfusion transduction protocol with adequate immune modulation would further enhance the rAAV8-mediated transduction strategy and lead to therapeutic benefits in DMD gene therapy.
Involvement of CD14 and β2-Integrins in Activating Cells with Soluble and Particulate Lipopolysaccharides and Mannuronic Acid Polymers (2000)

Lipopolysaccharide (LPS) and related bacterial products can be recognized by host inflammatory cells in a particulate, bacterium-bound form, as well as in various soluble, released forms. In the present study we have compared the mechanisms used by LPS, detoxified LPS (DLPS), and mannuronic acid polymers (M-polymers), in solution or covalently linked to particles, in stimulating monocytes to tumor necrosis factor (TNF) production. The addition of recombinant LPS binding protein (LBP) and/or soluble CD14 (sCD14) enhanced the production of TNF from monocytes stimulated with soluble LPS, DLPS, or M-polymer, but did not affect the response to M-polymer or DLPS attached to particles. Treatment of monocytes with antibody to CD14, CD18, or CD11b showed that CD14, but not CR3 (CD11b/CD18), mediated monocyte TNF production in response to the soluble antigens. In contrast, anti-CD14, anti-CD11b and anti-CD18 monoclonal antibodies all inhibited the response to the particulate stimuli. On the other hand, B975, a synthetic analog of Rhodobacter capsulatus lipid A, completely abrogated the monocyte TNF response induced by LPS but did not affect the TNF induction by DLPS or M-polymer, either in soluble or particulate forms. These data demonstrate that the engagement of immune receptors by bacterial products such as LPS, DLPS, and M-polymer is dependent upon the presentation form of their constituent carbohydrates, and that factors such as aggregation state, acylation, carbohydrate chain length, and solid versus liquid phase of bacterial ligands influence the mechanisms used by cells in mediating proinflammatory responses.
Potential role of ultrasound in anesthesia and intensive care (2011)

One of the most exiting recent technological advances in the field of anesthesia to track the region of interest is the introduction of anatomical evaluation by ultrasound imaging. Widespread use of this modality depends on its proven clinical efficacy, cost effectiveness, and practicality as it allows anesthesiologist to evaluate complex and varied anatomy prior to needle insertion. Sound used in medicine is not significantly transmitted by air or bone but through fluids which make up the larger part of soft tissues in the body. Ultrasound has been shown to offer excellent guidance for difficult venous access, epidural space identification in cases of difficult anatomy, delineating nerve plexuses for chronic nerve blocks, for regional anesthesia, and in transesophageal echocardiography for cardiac imaging with blood flows or in an otherwise high-risk patient where interventional procedure is required. It has special application to assess the narrowest diameter of the subglottic upper airway. A systemic literature search was performed in PubMed and the Cochrane library. The search strategy was set up using either single text word or combinations. We also included the studies where in these techniques were compared with conventional methods . Despite the initial excitement of this technique, ultrasound visualization is still indirect and images are subject to individual interpretation. It is gradually becoming routine in daily practice at our institution due to its reliability and safety. Though ultrasound is much safer, exposure in terms of intensity and time should be limited as far as possible, as high-energy ultrasound can cause heating and damage to tissues. In this review, we discuss established and future areas of ultrasound imaging and emphasize the use of B-mode ultrasound to improve the efficacy of interventional techniques. We have also illustrated potential uses with reference to cross-sectional B-mode images which visually represent a slice of tissues and are the easiest images for interpretation by clinicians.