gebhart/patrepeval huggingface dataset:
Representing Formal Languages: A Comparison Between Finite Automata and\n Recurrent Neural Networks (2019)

We investigate the internal representations that a recurrent neural network\n(RNN) uses while learning to recognize a regular formal language. Specifically,\nwe train a RNN on positive and negative examples from a regular language, and\nask if there is a simple decoding function that maps states of this RNN to\nstates of the minimal deterministic finite automaton (MDFA) for the language.\nOur experiments show that such a decoding function indeed exists, and that it\nmaps states of the RNN not to MDFA states, but to states of an {\\em\nabstraction} obtained by clustering small sets of MDFA states into\n"superstates". A qualitative analysis reveals that the abstraction often has a\nsimple interpretation. Overall, the results suggest a strong structural\nrelationship between internal representations used by RNNs and finite automata,\nand explain the well-known ability of RNNs to recognize formal grammatical\nstructure.\n
The heat capacity of proteins (1995)

The heat capacity plays a major role in the determination of the energetics of protein folding and molecular recognition. As such, a better understanding of this thermodynamic parameter and its structural origin will provide new insights for the development of better molecular design strategies. In this paper we have analyzed the absolute heat capacity of proteins in different conformations. The results of these studies indicate that three major terms account for the absolute heat capacity of a protein: (1) one term that depends only on the primary or covalent structure of a protein and contains contributions from vibrational frequencies arising from the stretching and bending modes of each valence bond and internal rotations; (2) a term that contains the contributions of noncovalent interactions arising from secondary and tertiary structure; and (3) a term that contains the contributions of hydration. For a typical globular protein in solution the bulk of the heat capacity at 25 degrees C is given by the covalent structure term (close to 85% of the total). The hydration term contributes about 15 and 40% to the total heat capacity of the native and unfolded states, respectively. The contribution of non-covalent structure to the total heat capacity of the native state is positive but very small and does not amount to more than 3% at 25 degrees C. The change in heat capacity upon unfolding is primarily given by the increase in the hydration term (about 95%) and to a much lesser extent by the loss of noncovalent interactions (up to approximately 5%).(ABSTRACT TRUNCATED AT 250 WORDS)
Generalized Titanate Ceramic Waste Form for Advanced Purex Reprocessing (2001)

Alternative dissolution processes for spent nuclear fuel lead to highly active waste streams rich in zirconium, iron, chromium, and nickel at levels that vary with fuel assembly design. A titanate ceramic phase assemblage has been developed with the flexibility to accommodate these variations in waste stream composition. Waste loadings range from 42 to 50 wt%. Leach rates are comparable to those from Synroc C.
Characteristics of cathelicidin-Bg, a novel gene expressed in the ear-side gland of Bufo gargarizans (2016)

The traditional Chinese medicine Chan Su (toad venom) comprises dried secretions of the ear-side gland of Bufo gargarizans. Chan Su is known for its small molecular components, which include telocinobufagin, marinobufagin, and bufalin, while in other amphibians, studies mainly focus on peptide components. Until recently, no genes expressed in the ear-side gland of B. gargarizans gland had been cloned. In this study, cathelicidin-Bg, a coding sequence of anti-microbial peptide (AMP), was cloned. The predicted amino acid sequence of cathelicidin-Bg was very similar to that from other amphibians, with a 34-amino acid mature peptide predicted in the C-terminus. The functions of this mature peptide were verified by microbe and tumor cell inhibition assays. Our results showed that the mature peptide of cathelicidin-Bg could inhibit the proliferation of Staphylococcus aureus and Pseudomonas aeruginosa. The mature peptide was also shown to selectively inhibit tumor cells. These results indicate that the identified coding sequence represents an active peptide of Chan Su.
Proteomic Analysis of Protein Phosphorylations in Heat Shock Response and Thermotolerance (2002)

Heat shock (HS) induces a wide variety of biological processes, including inhibition of protein synthesis, elevated expression of heat shock proteins, induction of thermotolerance, and apoptotic cell death in a dose-dependent manner. We compared phosphorylated proteins in heat-shocked and thermotolerant cells using proteome analysis. After HS treatment of control RIF-1 and their thermotolerant derivatives, TR-RIF-1 cells, cellular proteins were separated by two-dimensional gel electrophoresis and the phosphorylated proteins were detected with the anti-phosphotyrosine antibodies. We found that 93 proteins showed significant changes in phosphorylation between control and thermotolerant cells as a function of recovery time after HS; we identified 81 of these proteins with peptide mass fingerprinting using MALDI-TOF MS after in-gel trypsin digestion. These phosphorylated proteins exhibit various cellular functions, including chaperones, ion channels, signaling molecules, in transcription and translation processes, in amino acid biosynthesis, oxidoreduction, energy metabolism, and cell motility or structure, suggesting that HS turns on the various signaling pathways by activating protein-tyrosine kinases (PTKs). Of these, 20 proteins were previously identified phosphorylated proteins and 64 were newly identified. These proteins can be grouped into three families: 1) proteins highly phosphorylated in TR-RIF-1 cells at basal level and phosphorylated more significantly by HS in RIF-1 than TR-RIF-1; 2) proteins highly phosphorylated in control RIF-1 cells at basal level and phosphorylated more easily by HS in TR-RIF-1 than in RIF-1 cells; and 3) proteins with a similar basal phosphorylation level in both RIF-1 and TR-RIF-1 cells and responding to HS similarly in both cells. Most of the phosphorylated proteins are presumably involved in HS signaling in different ways, with the first and second families of proteins influencing thermotolerance. The possible tyrosine phosphorylation sites, the possible PTKs phosphorylating these proteins, and the proteins binding to these phosphorylated sites were predicted by the Netphos, ScanProsite, and Scansite programs. These results suggest that HS can activate various PTKs and HS responses can be regulated by phosphorylations of proteins having various functions.
Kyphectomy Using a Surgical Threadwire (T-saw) for Kyphotic Deformity in a Child With Myelomeningocele (2003)

For this child with myelomeningocele, kyphectomy using a surgical threadwire (T-saw) provided a satisfactory result without any major complication.
The cell polarity protein Vangl2 in the muscle shapes the neuromuscular synapse by binding to and regulating the tyrosine kinase MuSK (2022)

The development of the neuromuscular junction (NMJ) requires dynamic trans-synaptic coordination orchestrated by secreted factors, including Wnt family morphogens. To investigate how these synaptic cues in NMJ development are transduced, particularly in the regulation of acetylcholine receptor (AChR) accumulation in the postsynaptic membrane, we explored the function of Van Gogh-like protein 2 (Vangl2), a core component of Wnt planar cell polarity signaling. We found that conditional, muscle-specific ablation of <i>Vangl2</i> in mice reproduced the NMJ differentiation defects seen in mice with global <i>Vangl2</i> deletion. These alterations persisted into adulthood and led to NMJ disassembly, impaired neurotransmission, and deficits in motor function. Vangl2 and the muscle-specific receptor tyrosine kinase MuSK were functionally associated in Wnt signaling in the muscle. Vangl2 bound to and promoted the signaling activity of MuSK in response to Wnt11. The loss of <i>Vangl2</i> impaired RhoA activation in cultured mouse myotubes and caused dispersed, rather than clustered, organization of AChRs at the postsynaptic or muscle cell side of NMJs in vivo. Our results identify Vangl2 as a key player of the core complex of molecules shaping neuromuscular synapses and thus shed light on the molecular mechanisms underlying NMJ assembly.
In vivo lactate and β‐hydroxybutyrate editing using a pure‐phase refocusing pulse train (1998)

A refocusing pulse train consisting of a semiselective refocusing pulse and a selective inversion pulse to obtain a pure-phase refocusing at the frequency of maximal excitation of the semiselective refocusing pulse is proposed and applied to in vivo lactate and beta-hydroxybutyrate editing using difference spectroscopy. It is shown, using both rotation matrix theory and phantom experiments, that the soft inversion pulse has to be halved to flank the semiselective pulse to obtain perfect refocusing and cancellation of interfering resonances. The editing method is used to obtain lactate and beta-hydroxybutyrate spectra from the occipital cortex of juvenile epilepsy patients before and after ketogenic diet treatment.
ChemInform Abstract: Activation of Phosphines with Borane. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
327 Symptom Relief and Sexual Function Improvement for Patients with All Types of Prostate Enlargement after Prostatic Urethral Lift (PUL) (2020)

Surgical treatments for BPH carry lengthy recovery times and sizeable rates of ejaculatory dysfunction. In contrast, the Prostatic Urethral Lift (PUL) has been shown to deliver rapid and significant symptom improvement with low morbidity and preservation of sexual function. To evaluate symptom response and sexual function results of PUL across all types of prostate enlargement including obstructive median lobe (OML) the MedLift trail was undertaken. MedLift was an FDA extension of the L.I.F.T. randomized study. Forty-five men age ≥ 50 with International Prostate Symptom Score (IPSS) ≥ 13, peak flow rate (Qmax) ≤ 12 ml/s and prostate volume 30-80 cc were enrolled. Inclusion criteria were identical to the L.I.F.T. study except for requiring an OML. Symptom relief, quality of life (QoL), Qmax, and sexual function were evaluated through 12 months. These outcomes were also combined with the L.I.F.T. Lateral Lobe (LL) only results to assess the effectiveness of PUL across a group of men with all types of prostate enlargement.
Distribution and Elimination of [2-14C]Amino-3, 8-Dimethylimidazo [4, 5-f] quinoxaline in Mice. Analysis by Whole Animal Autoradiography (1991)

1. 2-Amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) is a potent bacterial promutagen and carcinogen, formed when beef is cooked. In mammals, MeIQx is metabolized and activated by liver enzymes, but induces tumours in both hepatic and extrahepatic tissues. 2. Intravenous administration of [14C]MeIQx and whole animal autoradiography has been employed to examine the disposition of MeIQx. Within 10 min, radiolabel was distributed throughout body tissue. Liver levels of radioactivity rapidly rose and remained elevated in comparison to other tissues, throughout the period of study (4 d). 3. At early time points radioactivity accumulated in the stomach, kidney and salivary glands then later in the intestine. Radioactivity was rapidly eliminated from the majority of tissues although did persist in liver and intestines throughout the duration of the study, probably due to covalently bound material. No radioactivity could be detected in the central nervous system, thus neither MeIQx nor its metabolites cross the blood-brain barrier to any significant extent. 4. The rapid elimination of radioactivity from the tissues is in good agreement with the time course of excretion of MeIQx. Irrespective of the route of administration (i.v., i.p., p.o.), a substantial proportion of the labelled material is excreted within 24 h and is present in both urine and faeces in similar quantities. 5. Thus MeIQx is extensively bioavailable, is distributed throughout body tissue and, although the majority is quickly cleared, some remains bound to liver and intestine.
Adrenergic regulation of a key cardiac potassium channel can contribute to atrial fibrillation: evidence from an IKs transgenic mouse (2007)

Inherited gain-of-function mutations of genes coding for subunits of the heart slow potassium (I Ks) channel can cause familial atrial fibrillation (AF). Here we consider a potentially more prevalent mechanism and hypothesize that beta-adrenergic receptor (beta-AR)-mediated regulation of the I Ks channel, a natural gain-of-function pathway, can also lead to AF. Using a transgenic I Ks channel mouse model, we studied the role of the channel and its regulation by beta-AR stimulation on atrial arrhythmias. In vivo administration of isoprenaline (isoproterenol) predisposes I Ks channel transgenic mice but not wild-type (WT) littermates that lack I Ks to prolonged atrial arrhythmias. Patch-clamp analysis demonstrated expression and isoprenaline-mediated regulation of I Ks in atrial myocytes from transgenic but not WT littermates. Furthermore, computational modelling revealed that beta-AR stimulation-dependent accumulation of open I Ks channels accounts for the pro-arrhythmic substrate. Our results provide evidence that beta-AR-regulated I Ks channels can play a role in AF and imply that specific I Ks deregulation, perhaps through disruption of the I Ks macromolecular complex necessary for beta-AR-mediated I Ks channel regulation, may be a novel therapeutic strategy for treating this most common arrhythmia.
Automatic Generation and Insertion of Assessment Items in Online Video Courses (2015)

In this paper, we propose a prototype system for automatic generation and insertion of assessment items in online video courses. The proposed system analyzes text transcript of a requested video lecture to suggest self-assessment items in runtime through automatic discourse segmentation and question generation. To deal with the problem of question generation from noisy transcription, the system relies on semantically similar Wikipedia text segments. We base our study on a popular video lecture portal - National Programme on Technology Enhanced Learning (NPTEL). However, it can be adapted to other portals as well.
Assessment of approximations in nonequilibrium Green’s function theory (2011)

A nonequilibrium Green's function (NEGF) method for stationary carrier dynamics in open semiconductor nanodevices is presented that includes all relevant incoherent scattering mechanisms. A consistent lead model is developed that ensures all observables to reflect intrinsic device properties. By restricting the charge self-consistent calculations to vertical transport through heterostructures, the Green's functions and self-energies can be determined very accurately. This allows us to assess many commonly used approximations, such as ballistic leads, decoupling of Dyson's and Keldysh's equations, truncated or momentum-averaged self-energies, and local self-energies in the NEGF formalism in detail, and to study limiting cases such as diffusive transport in resistors. The comparison of exact and approximated NEGF calculations illustrates the physical implications and validity of common approximations and suggests numerically efficient simplifications.
An imaging colorimeter for noncontact tissue color mapping (1997)

There has been a considerable effort in several medical fields, for objective color analysis and characterization of biological tissues. Conventional colorimeters have proved inadequate for this purpose, since they do not provide spatial color information and because the measuring procedure randomly affects the color of the tissue. In this paper an imaging colorimeter is presented, where the nonimaging optical photodetector of colorimeters is replaced with the charge-coupled device (CCD) sensor of a color video camera, enabling the independent capturing of the color information for any spatial point within its field-of-view. Combining imaging and colorimetry methods, the acquired image is calibrated and corrected, under several ambient light conditions, providing noncontact reproducible color measurements and mapping, free of the errors and the limitations present in conventional colorimeters. This system was used for monitoring of blood supply changes of psoriatic plaques, that have undergone Psoralens and ultraviolet-A radiation (PUVA) therapy, where reproducible and reliable measurements were demonstrated. These features highlight the potential of the imaging colorimeters as clinical and research tools for the standardization of clinical diagnosis and for the objective evaluation of treatment effectiveness.
Effect of ICRF-193, a novel DNA topoisomerase II inhibitor, on simian virus 40 DNA and chromosome replication in vitro. (1992)

The effect of ICRF-193, a noncleavable-complex-forming topoisomerase II inhibitor, on simian virus 40 (SV40) DNA and SV40 chromosome replication was examined by using an in vitro replication system composed of HeLa cell extracts and SV40 T antigen. Unlike the topoisomerase inhibitors VP-16 and camptothecin, ICRF-193 had little effect on DNA chain elongation during SV40 DNA replication, but high-molecular-weight DNAs instead of segregated monomer DNAs accumulated as major products. Analysis of the high-molecular-weight DNAs by two-dimensional gel electrophoresis revealed that they consisted of catenated dimers and late Cairns-type DNAs. Incubation of the replicated DNA with topoisomerase II resulted in conversion of the catenated dimers to monomer DNAs. These results indicate that ICRF-193 induces accumulation of catenated dimers and late Cairns-type DNAs by blocking the decatenating and relaxing activities of topoisomerase II in the late stage of SV40 DNA replication. In contrast, DNA replication of SV40 chromosomes was severely blocked by ICRF-193 at the late stage, and no catenated dimers were synthesized. These results are consistent with the finding that topoisomerase II is required for unwinding of the final duplex DNA in the late stage of SV40 chromosome replication in vitro.
Removable damping treatments for use in sheet metal fabrication (2015)

Many industrial fabrication processes on metallic structures generate a great deal of work place noise. For example, riveting and chiseling on light-weight, stiff aerospace structures such as fusalage components and flight surfaces subject the workpiece to repeated impacts and consequent noise generation. Many such structures may be lightly damped. Many damping treatments are targeted toward permanent installation on a structure, but if the treatments are considered to be removable, one has design freedoms including placement on a structure, as well as mass and damping means, that might not otherwise exist if the treatment had to remain in place. A shot-mass or particle-impact damper configured in an elastic, cellular array is shown to provide high loss factors and mass loading, which, along with ease of placement and removal, may provide significant reduction in component vibration during fabrication and consequent reduction in noise in the work place. The concept applied to an example aircraft panel when subjected to riveting operations yields more than 10 dB of noise reduction.
ChemInform Abstract: Active Carbon‐Supported Aluminium Copper(I) Chloride as Solid Carbon Monoxide Adsorbent. (1986)

Abstract Active carbon‐supponed AlCuCl 4 (preparation is described) rapidly adsorbs CO at 20°C from a 9:1 CO‐ N 2 mixture and the equilibrium molar ratio of adsorbed CO to AlCuCl 4 is 1.03.
Specification of R7, cone and inter-ommatidial pigment cells in GFP-PAST1B transgenic flies. (2017)

&lt;p&gt;(A) Staining of GMRGal4&gt;UAS-GFP-PAST1B (GFP appears as grey, or green in the merge, in all the panels) (line 1), early-mid pupa eyes (42-48h after puparium formation) with Elav (grey, or red in the merge) and pros (grey, or purple in the merge). The dotted circle represents an ommatidium with two R7 photoreceptors (B) Quantification of the number of R7 photoreceptors in early-mid pupa eyes of wild type (n = 249) and overexpressing transgenic PAST1B (line 1) (n = 145) ommatidium; &lt;i&gt;P&lt;/i&gt; &lt; 0.001. (C) Phalloidin (grey, or red in the merge) and cut (grey or purple in the merge) staining of mirrGal4&gt;UAS-GFP-PAST1B (line 1) early-mid pupa eyes (42-48h after puparium formation). The dotted circles represent ommatidia with five cone cells and the dotted square represents an ommatidium with three cone cells. Shown are Z-projections of confocal sections. (D) Quantification of the number of cone cells in early-mid pupal eyes of wild type (n = 189) and transgenic PAST1B (line 1) (n = 138) ommatidia; &lt;i&gt;P&lt;/i&gt; &lt; 0.002. (E) Phalloidin (grey, or red in the merge) and Dlg (grey, or purple in the merge) staining of mirrGal4&gt;UAS-GFP-PAST1B (line 1) early-mid pupa eyes (42-48h after puparium formation). The arrowhead marks an extra inter-ommatidial pigment cell.&lt;/p&gt;
Using Fos Imaging in the Rat to Reveal the Anatomical Extent of the Disruptive Effects of Fornix Lesions (2000)

Activity of the immediate early gene c-fos was compared across hemispheres in rats with unilateral fornix lesions. To engage Fos production, rats first performed a radial arm maze task that is severely disrupted by bilateral fornix lesions. Using immunohistochemical techniques, Fos-positive cells were visualized and counted in 39 sites in both hemispheres. Fornix lesions led to a significant reduction in Fos in all ipsilateral hippocampal subfields, as well as the entorhinal cortex and most of the subicular complex. Other sites that showed reduced activity included the ipsilateral retrosplenial, anterior cingulate, and postrhinal cortices. Subcortical regions showing significant Fos decreases included the anterior thalamic nuclei, supramammillary nucleus, diagonal band of Broca, and lateral septum. Thus, the effects of fornix lesions extended beyond the hippocampal formation and included sites not directly innervated by the tract. These changes were nevertheless selective, as shown by the lack of hemispheric difference in any of the preselected control sites, the perirhinal cortex, or nucleus accumbens. Furthermore, there were no hemispheric differences in an additional group of animals with unilateral fornix lesions that were killed directly from the home cage. The location of Fos changes closely corresponded to those brain regions that when lesioned disrupt spatial working memory. Moreover, there was a correspondence between those brain regions that show increased Fos production in normal animals performing the radial arm maze task and those affected by fornix lesions. These results show that fornix transection has widespread, but selective, effects on a network of structures normally activated by spatial memory processes, with these effects extending beyond the hippocampal formation.