gebhart/patrepeval huggingface dataset:
Retrovirus-Mediated Transduction of an Engineered Intron-Containing Purine Nucleoside Phosphorylase Gene (1995)

We constructed and tested several retroviral vectors containing abbreviated purine nucleoside phosphorylase (PNP) genes in the reverse orientation, a strategy compatible with transduction of intron-containing genes. We observed two types of deletions in these vectors after one round of replication: (i) Deletions flanked by direct repeats with one copy of the repeat retained in the provirus, presumably resulting from reverse transcriptase slippage during (-) strand DNA synthesis. (ii) Deletions due to fortuitous splice sites in the PNP complementary strand. Two splice donor sites and three splice acceptor sites were identified in a 3.0-kb PNP minigene. We found that the splice donor sites (but not the splice acceptor sites) could be predicted by sequence analysis of the PNP complementary strand. To increase the frequency of intact PNP gene transduction, we introduced sequence modifications: The putative PNP polyadenylation signal and a truncated 117-bp 3' flank were recovered from a rearranged provirus and inserted in place of a 1.2-kb genomic 3' flank. Sequences associated with deletions were eliminated from the PNP 5' untranslated region, and two fortuitous splice donor signals in the complementary strand were inactivated. A retroviral vector LN-PMG11, containing the engineered 2.9-kb PNP minigene in the reverse orientation, was transduced intact in 23% (5/22) of clones after one round of replication and in 87% (20/23) of clones after a second round of replication from two primary virus producer clones. Directed mutagenesis of sequences preventing intact retroviral transduction thus provided a 2.9-kb PNP gene that was transduced intact and expressed at a high level.
A Phosphonium Ylide as an Ionic Nucleophilic Catalyst for Primary Hydroxyl Group Selective Acylation of Diols (2017)

Carbonyl-stabilized phosphonium ylides exhibit great utility in modern organic synthesis, and they are known as an ambident nucleophile at the carbonyl oxygen atom and at the α-carbon atom. However, they have found limited use as catalysts. We focused on the inherent nucleophilicity of the oxygen atom to develop an ionic nucleophilic catalysis, and the phosphonium ylide-catalyzed primary alcohol selective acylation of mixed diols with acid anhydrides has been demonstrated. Mechanistic studies revealed the behavior of a catalyst, which would contribute to the field of ylide chemistry.
Fingerprint Enhancement Using Unsupervised Hierarchical Feature Learning (2014)

We present an approach for learning low- and high-level fingerprint structures in an unsupervised manner, which we use for enhancement of fingerprint images and estimation of orientation fields, frequency images, and region masks. We incorporate the use of a convolutional deep belief network to learn features from greyscale, clean fingerprint images. We also show that reconstruction performed by the learnt network works as a suitable enhancement of the fingerprint, and hierarchical probabilistic inference is able to estimate overall fingerprint structures as well. Our approach performs better than Gabor-based enhancement and short time Fourier transform-assisted enhancement on images it was trained on. We further use information from the learnt features in first layer, which are short and oriented ridge structures, to extract the orientation field, frequency image, and region mask of input fingerprints.
End-to-End Time-Sensitive Optical Networking: Challenges and Solutions (2019)

Time-sensitive applications, most notably, for 5G fronthauling and Industry 4.0, require deterministic (jitter-free) low-latency, highly reactive, and trustable networks, as opposed to today's best effort Internet. We review existing solutions, both established and at the research stage, and compare them for key next-generation 5G fronthauling and industrial requirements.
THE ABSORPTION OF PARTICLES BY THE LYMPHATICS OF THE DIAPHRAGM (1960)

The absorption of particles from the peritoneal cavity by the terminal lymphatics, or lacunes, of the rabbit's diaphragm has been studied with the light and electron microscopes. Absorption occurs predominantly through those parts of the peritoneal surface of the diaphragm which overlie the lymphatic lacunes. These parts are referred to as the lacunar roofs. The mesothelial cells of the roofs have features which distinguish them from mesothelial cells elsewhere on the peritoneal surface of the diaphragm. The cells are more closely set, stain more darkly, and separate from each other more readily, particularly at the base of the intercellular junctions. They are supported by a lattice of coarse and fine fibres. In the meshes of this lattice mesothelial and lymphatic endothelial cells are separated only by the basement membrane of the mesothelium which in places may be incomplete. Erythrocytes pass through the roof into the lumen of the lacune through gaps which are formed by separation of the mesothelial cells and of the endothelial cells at the intercellular junctions. Particles of India ink and colloidal particles of thorium dioxide and saccharated iron oxide enter the intercellular spaces of the mesothelium and spread freely within the meshes of the fibre lattice. These particles appear to pass through the mesothelium by a predominantly extracellular pathway and probably enter the lymphatic lumen through temporary channels which are formed by separation of endothelial cells at the intercellular junctions. Absorbed colloidal particles accumulate in the cytoplasm of mesothelial and lymphatic endothelial cells in the roofs and a proportion of absorbed material may be transported intracellularly through these two layers in cytoplasmic vesicles. Lymphatic endothelial cells at other sites in the diaphragm can take up colloidal particles from the lumen of the lymphatics.
Manganese-Induced Parkinsonism and Parkinson’s Disease: Shared and Distinguishable Features (2015)

Manganese (Mn) is an essential trace element necessary for physiological processes that support development, growth and neuronal function. Secondary to elevated exposure or decreased excretion, Mn accumulates in the basal ganglia region of the brain and may cause a parkinsonian-like syndrome, referred to as manganism. The present review discusses the advances made in understanding the essentiality and neurotoxicity of Mn. We review occupational Mn-induced parkinsonism and the dynamic modes of Mn transport in biological systems, as well as the detection and pharmacokinetic modeling of Mn trafficking. In addition, we review some of the shared similarities, pathologic and clinical distinctions between Mn-induced parkinsonism and Parkinson's disease. Where possible, we review the influence of Mn toxicity on dopamine, gamma aminobutyric acid (GABA), and glutamate neurotransmitter levels and function. We conclude with a survey of the preventive and treatment strategies for manganism and idiopathic Parkinson's disease (PD).
Necrotizing Enterocolitis: Review of State-of-the-Art Imaging Findings with Pathologic Correlation (2007)

Plain abdominal radiography is the current standard imaging modality for evaluation of necrotizing enterocolitis (NEC). Sonography is still not routinely used for diagnosis and follow-up, as it is not widely recognized that it can provide information that is not provided by plain abdominal radiography and that may affect the management of NEC. Like plain abdominal radiography, sonography can depict intramural gas, portal venous gas, and free intraperitoneal gas. However, the major advantages of abdominal sonography over plain abdominal radiography are that it can depict intraabdominal fluid, bowel wall thickness, and bowel wall perfusion. Sonography may depict changes consistent with NEC when the plain abdominal radiographic findings are nonspecific and inconclusive. Thinning of the bowel wall and lack of perfusion at sonography are highly suggestive of nonviable bowel and may be seen before visualization of pneumoperitoneum at plain abdominal radiography. The mortality rate is higher after perforation; thus, earlier detection of severely ischemic or necrotic bowel loops, before perforation occurs, could potentially improve the morbidity and mortality in NEC. The information provided by sonography allows a more complete understanding of the state of the bowel in patients with NEC and may thus make management decisions easier and potentially change outcome.
Frequency Shifts of the Internal Phonon Modes in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">La</mml:mi></mml:mrow><mml:mrow><mml:mn>0.7</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ca</mml:mi></mml:mrow><mml:mrow><mml:mn>0.3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Mn<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1996)

Infrared reflectivity spectra were measured for a polycrystalline ${\mathrm{La}}_{0.7}$${\mathrm{Ca}}_{0.3}$Mn${\mathrm{O}}_{3}$ sample. The internal phonon modes, i.e., the bending and stretching modes, of the Mn${\mathrm{O}}_{6}$ octahedra show significant frequency shifts near the Curie temperature ${T}_{C}$. The frequency shifts of the internal phonon modes were found to have a linear relationship with the excess lattice expansion above ${T}_{C}$, which deviates from a prediction of the Gr\"uneisen law. A strong electron-phonon coupling and a crossover from small to large polaronic states are attributed to the observed frequency shifts.
Real-time footstep planning for humanoid robots among 3D obstacles using a hybrid bounding box (2012)

In this paper we introduce a new bounding box method for footstep planning for humanoid robots. Similar to the classic bounding box method (which uses a single rectangular box to encompass the robot) it is computationally efficient, easy to implement and can be combined with any rigid body motion planning library. However, unlike the classic bounding box method, our method takes into account the stepping over capabilities of the robot, and generates precise leg trajectories to avoid obstacles on the ground. We demonstrate that this method is well suited for footstep planning in cluttered environments.
Range measurement using dynamic fringe protection (1988)

A novel technique using dynamic fringe projection is discussed and the methods of analysis of the waveforms generated by such an instrument are given. An error analysis of the range equation is included to ensure that the design of such a system may be optimised for the minimisation of range errors.
Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter (2005)

A Gram-negative bacterium, designated LA31B(T), was isolated from water collected from a hypersaline lagoon on Laysan Atoll in the north-western Hawaiian Islands. Single cells of LA31B(T) were slightly curved but became helical as their length increased. Preliminary characterization based on 16S rRNA gene sequence analysis showed that LA31B(T) shared 96.0 % identity with an Arcobacter sp. isolated from a cyanobacterial mat in hypersaline Lake Sinai, and 94 % identity with Arcobacter nitrofigilis, the type species of the genus Arcobacter. A polyphasic taxonomic study was conducted and confirmed the phylogenetic affiliation of strain LA31B(T) to the genus Arcobacter. However, LA31B(T) was found to be distinct from all recognized Arcobacter species, by a comprehensive biochemical test analysis, whole-cell fatty acid profiling, DNA G + C content (35 mol% in LA31B(T)) and degree of DNA-DNA reassociation. Most notably, LA31B(T) was found to be an obligate halophile, a hitherto undescribed feature among recognized Arcobacter species. These data indicate that LA31B(T) should be considered to represent a novel species in the genus Arcobacter, for which the name Arcobacter halophilus sp. nov. is proposed. This is the first obligately halophilic member of the genus. The type strain is LA31B(T) (=ATCC BAA-1022(T) = CIP 108450(T)).
A field-portable thermal infrared grating spectrometer (THIRSPEC) (1994)

A thermal infrared grating spectrometer was developed for field studies in the Earth sciences. The design is based on a reflection grating and a 60-element HgCdTe detector array. The useful spectral range of the instrument covers 7.9-11.3 /spl mu/m with a Nyquist limited resolution of 0.16 /spl mu/m. The instrument averages over a 12/spl deg/ field of view and compares the exitance of the target to that of an internal black body at ambient temperature. The noise equivalent temperature is approximately 0.06/spl deg/K over the useful spectral range. Background radiance reflected from the surface of the target can seriously impede the determination of emissivity. This effect is removed from the spectra of geological samples by the use of reference samples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Functional Electrical Stimulation for Treatment of Chronic Foot Drop Due to an Incomplete Sacral Nerve Root Lesion: A Case Study (2010)

The Foot
The Unimportance of Precedence in the Law of Federal Courts (1990)

Part I of this Article asserts that the Supreme Court pays little attention to precedent in federal courts law. My examples in support of this claim are taken from important areas of federal courts doctrine, where two major upheavals have taken place in the past thirty years. First, the Warren Court rewrote the law to expand access to federal court. then under Chief Justice Burger, the Court undid many of the changes wrought by its predecessor. The discussion in Part I of prominent departures from precedent is not offered as decisive proof that stare decisis is less important in federal courts cases than elsewhere. It is instead an account of the grounds for my intuition that this is so. I do not know how to go about empirically proving the point, short of developing a means of precisely measuring the importance of precedent in various areas, and then persuading the world to accept my methodology. I am not up to that task. Part II examines the concept of precedent in general terms. Borrowing from the jurisprudential literature on stare decisis, I argue that precedent is best viewed as means and not an end in itself. Adherence to prior cases is a way to pursue a number of goals, including predictability in the law, efficiency in decisionmaking, and fairness to litigants. These worthy goals come at a price, for a court that chooses precedent as its rule of decision necessarily foregoes the opportunity to improve the content of the law by reexamining the arguments on the merits of the legal question at hand. Part III considers the implications of this cost-benefit approach to precedent for federal courts law. The values of predictability, efficiency, and fairness carry great weight in cases where the legal rules bear heavily on primary behavior and the substantive law of rights and obligations. But they are not particularly strong in the law of federal courts, where the issue is typically the distribution of decisionmaking power between federal and state courts and among courts and other governmental institutions A court bent on reforming the law will always find it comparatively easy to justify a departure from precedent in federal courts law. In addition, the costs of adhering to precedent here are substantial. Although federal courts doctrine rarely bears directly on the substantively law of rights and obligations, it does address important question of governmental structure. It is concerned with the institutional role of the federal courts in our system of government. Fidelity to precedent would impose a high cost on Supreme Court Justices, for it would oblige them to pass up the opportunity to contribute to the development of law on these vital matters. As a result of this combination of factors, the Supreme Court will find, more often than courts do in other areas of the law, that the costs of following precedent are especially high and the benefits especially low in the adjudication of federal courts issues.
Flexible metamaterial absorbers for stealth applications at terahertz frequencies (2011)

We have wrapped metallic cylinders with strongly absorbing metamaterials. These resonant structures, which are patterned on flexible substrates, smoothly coat the cylinder and give it an electromagnetic response designed to minimize its radar cross section. We compare the normal-incidence, small-beam reflection coefficient with the measurement of the far-field bistatic radar cross section of the sample, using a quasi-planar THz wave with a beam diameter significantly larger than the sample dimensions. In this geometry we demonstrate a near-400-fold reduction of the radar cross section at the design frequency of 0.87 THz. In addition we discuss the effect of finite sample dimensions and the spatial dependence of the reflection spectrum of the metamaterial.
Effects of probiotic and prebiotic on gastrointestinal motility in newborns. (2009)

To fortify the biological role of milk formula has been suggested to use probiotics and prebiotics as functional components to mimic the effect of breast milk. The aim of this study was to evaluate the effects of prebiotic, probiotic added to a standard formula on gastrointestinal motility respect to placebo-formula. Cutaneous electrogastrography (EGG) and ultrasound gastric emptying (GE) were performed in 49 preterm newborns. 17 newborns were exclusively breast-fed; 32 were randomly assigned to receive prebiotic-added formula (0.8 g/dl of a mixture from scGOS and lcFOS, ratio 9:1) (10), a probiotic-added formula (L. reuteri at dose of 1x10(8) colony forming units (CFU) per day) (10), a formula with placebo (12) for 30 days. No difference was seen in the nutritional parameters and no adverse events were reported. After the intervention period, the prebiotic, probiotic, and breast milk groups showed a higher percentage of EGG slow wave propagation and faster gastric half emptying time respect to placebo group (ANOVAon ranks p<0.001; Dunn test vs control: prebiotic, probiotic and breast-milk vs placebo formula p<0.05; and ANOVA on ranks p=0.005; Dunn test vs control: prebiotic, probiotic and breast-milk vs placebo formula p<0.05, respectively). Feeding preterm infants with a formula supplemented with prebiotics or probiotics may stimulate gastric emptying and improve maturation of the EGG activity mimicking the effect of breast milk.
Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies (2015)

Regulatory RNAs have become integral components of the synthetic biology and bioengineering toolbox for controlling gene expression. We recently expanded this toolbox by creating small transcription activating RNAs (STARs) that act by disrupting the formation of a target transcriptional terminator hairpin placed upstream of a gene. While STARs are a promising addition to the repertoire of RNA regulators, much work remains to be done to optimize the fold activation of these systems. Here we apply rational RNA engineering strategies to improve the fold activation of two STAR regulators. We demonstrate that a combination of promoter strength tuning and multiple RNA engineering strategies can improve fold activation from 5.4-fold to 13.4-fold for a STAR regulator derived from the pbuE riboswitch terminator. We then validate the generality of our approach and show that these same strategies improve fold activation from 2.1-fold to 14.6-fold for an unrelated STAR regulator, opening the door to creating a range of additional STARs to use in a broad array of biotechnologies. We also establish that the optimizations preserve the orthogonality of these STARs between themselves and a set of RNA transcriptional repressors, enabling these optimized STARs to be used in sophisticated circuits.
Radar-interference-based bridge identification for collision avoidance systems (2011)

Automotive radar sensors are commonly used for providing environment information required by driver assistance systems. Although they show a good performance in measuring the distance and the speed of other objects even under poor weather conditions, they suffer from the shortcoming of a missing resolution in elevation. Consequently bridges crossing the lane of the ego vehicle may look similar to stationary obstacles. This contribution shows a bridge identification algorithm based on the interference pattern resulting from the multipath propagation of the radar wave. During the approaching to bridges or stationary obstacles, the pattern leads to a variation in the backscattered power from the object. This variation can be used to make statements about the object height position above the road. Results calculated from real scanning radar sensor data show the usability in real traffic scenarios.
Direct Development of Functionally Mature Tryptase/Chymase Double-Positive Connective Tissue-Type Mast Cells from Primate Embryonic Stem Cells (2007)

Conditions that influence the selective development or recruitment of connective tissue-type and mucosal-type mast cells (MCs) are not well understood. Here, we report that cynomolgus monkey embryonic stem (ES) cells cocultured with the murine aorta-gonad-mesonephros-derived stromal cell line AGM-S1 differentiated into cobblestone (CS)-like cells by day 10-15. When replated onto fresh AGM-S1 with the addition of stem cell factor, interleukin-6, and Flt3 ligand, these CS-like cells displayed robust growth and generated almost 100% tryptase/chymase double-positive MCs within 3 weeks. At all time points, the percentage of tryptase-positive cells did not exceed that of chymase-positive cells. These ES-derived MCs were CD45+/Kit+/CD31+/CD203c+/HLA-DR- and coexpressed a high-affinity IgE receptor on their surface, which was upregulated after IgE exposure. Electron microscopy showed that they contained many electron dense granules. Moreover, ES-derived MCs responded to stimulation by via IgE and substance P by releasing histamine. These results indicate that ES-derived MCs have the phenotype of functionally mature connective tissue-type MCs. The rapid maturation of ES-derived MCs suggests a unique embryonic pathway in primates for early development of connective tissue-type MCs, which may be independent from the developmental pathway of mucosal-type MCs.
Genome Sequence of <i>Lactobacillus amylovorus</i> GRL1112 (2010)

Lactobacillus amylovorus is a common member of the normal gastrointestinal tract (GIT) microbiota in pigs. Here, we report the genome sequence of L. amylovorus GRL1112, a porcine feces isolate displaying strong adherence to the pig intestinal epithelial cells. The strain is of interest, as it is a potential probiotic bacterium.