gebhart/patrepeval huggingface dataset:
Nucleotide sequence of the gene for the M r 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M r 38,950 (1982)

The gene for the so-called M(r) 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is approximately 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of M(r) 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of M(r) 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA.
Prox1 postmitotically defines dentate gyrus cells by specifying granule cell identity over CA3 pyramidal cell fate in the hippocampus (2012)

The brain is composed of diverse types of neurons that fulfill distinct roles in neuronal circuits, as manifested by the hippocampus, where pyramidal neurons and granule cells constitute functionally distinct domains: cornu ammonis (CA) and dentate gyrus (DG), respectively. Little is known about how these two types of neuron differentiate during hippocampal development, although a set of transcription factors that is expressed in progenitor cells is known to be required for the survival of granule cells. Here, we demonstrate in mice that Prox1, a transcription factor constitutively expressed in the granule cell lineage, postmitotically functions to specify DG granule cell identity. Postmitotic elimination of Prox1 caused immature DG neurons to lose the granule cell identity and in turn terminally differentiate into the pyramidal cell type manifesting CA3 neuronal identity. By contrast, Prox1 overexpression caused opposing effects on presumptive hippocampal pyramidal cells. These results indicate that the immature DG cell has the potential to become a granule cell or a pyramidal cell, and Prox1 defines the granule cell identity. This bi-potency is lost in mature DG cells, although Prox1 is still required for correct gene expression in DG granule cells. Thus, our data indicate that Prox1 acts as a postmitotic cell fate determinant for DG granule cells over the CA3 pyramidal cell fate and is crucial for maintenance of the granule cell identity throughout the life.
Direct Catalytic Asymmetric Mannich Reactions of Malonates and β‐Keto Esters (2003)

The first catalytic asymmetric direct Mannich reaction of malonates and beta-keto esters has been developed. Malonates react with an activated N-tosyl-alpha-imino ester catalyzed by chiral tert-butyl-bisoxazoline/Cu(OTf)(2) to give the Mannich adducts in high yields and with up to 96% ee. These reactions create a chiral quaternary carbon center and it is demonstrated that this new direct Mannich reactions provides for example a new synthetic procedure for the formation of optically active beta-carboxylic ester alpha-amino acid derivatives. A series of different beta-keto esters with various ester substituents has been screened as substrates for the catalytic asymmetric direct Mannich reaction and it was found that the best results in terms of yield, diastereo- and enantioselectivity were obtained when tert-butyl esters of beta-keto esters were used as the substrate. The reaction of different beta-keto tert-butyl esters with the N-tosyl-alpha-imino ester gave the Mannich adducts in high yields, diastereo- and enantioselectivities (up to 95% ee) in the presence of chiral tert-butyl-bisoxazoline/Cu(OTf)(2) as the catalyst. To expand the synthetic utility of this direct Mannich reaction a diastereoselective decarboxylation reaction was developed for the Mannich adducts leading to a new synthetic approach to attractive optically active beta-keto alpha-amino acid derivatives. Based on the stereochemical outcome of the reactions, various approaches of the N-tosyl-alpha-imino ester to the chiral bisoxazoline/Cu(II)-substrate intermediate are discussed.
The Role of Colloid Interactions in Solid-Liquid Separation (1993)

Forces between particles in water become especially important when the particles are in the colloidal size range (less than a few mm). To a first approximation inter-particle forces or colloid interactions are linearly dependent on particle size and they become stronger, relative to external forces, as particle size decreases. The separation of fine particles from water by processes such as coagulation, filtration and flotation can be crucially dependent on the manipulation of colloid interactions, usually to promote attachment of particles to each other or to surfaces. The most important types of colloid interaction are briefly discussed. These include van der Waals forces, electrical interaction, hydration forces, hydrophobic interaction and effects associated with adsorbed polymers, such as steric repulsion and polymer bridging. These are all short-range interactions, which have little influence on the transport of particles but which can have a major effect on collision efficiencies and on the adhesion between particles. Some examples of solid-liquid separation processes in which colloid interactions are important are given.
Regulation of high‐affinity leucine transport in escherichia coli (1980)

Leucine is transported into E coli by two osmotic shock-sensitive, high-affinity systems (LIV-I and leucine-specific systems) and one membrane bound, low-affinity system (LIV-II). Expression of the high-affinity transport systems is altered by mutations in livR and 1stR, genes for negatively acting regulatory elements, and by mutations in rho, the gene for transcription termination. All four genes for high-affinity leucine transport (livJ, livK, livH, and livG) are closely linked and have been cloned on a plasmid vector, pOX1. Several subcloned fragments of this plasmid have been prepared and used in complementation and regulation studies. The results of these studies suggest that livJ and livK are separated by approximately one kilobase and give a gene order of livJ-livK-livH. livJ and livK appear to be regulated in an interdependent fashion; livK is expressed maximally when the livJ gene is activated by mutation or deletion. The results support the existence of separate promotors for the livJ and livK genes. The effects of mutations in the rho and livR genes are additive on one another and therefore appear to be involved in independent regulatory mechanisms. Mutations in the rho gene affect both the LIV-I and leucine-specific transport systems by increasing the expression of livJ and livK, genes for the LIV-specific and leucine-specific binding proteins, respectively.
A Neuromorphic Cortical-Layer Microchip for Spike-Based Event Processing Vision Systems (2006)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We present a neuromorphic cortical-layer processing microchip for address event representation (AER) spike-based processing systems. The microchip computes 2-D convolutions of video information represented in AER format in real time. AER, as opposed to conventional frame-based video representation, describes visual information as a sequence of events or spikes in a way similar to biological brains. This format allows for fast information identification and processing, without waiting to process complete image frames. The neuromorphic cortical-layer processing microchip presented in this paper computes convolutions of programmable kernels over the AER visual input information flow. It not only computes convolutions but also allows for a programmable forgetting rate, which in turn allows for a bio-inspired coincidence detection processing. Kernels are programmable and can be of arbitrary shape and arbitrary size of up to 32&lt;formula formulatype="inline"&gt; &lt;tex&gt;$~\times~$&lt;/tex&gt;&lt;/formula&gt;32 pixels. The convolution processor operates on a pixel array of size 32&lt;formula formulatype="inline"&gt;&lt;tex&gt;$~\times~$&lt;/tex&gt; &lt;/formula&gt;32, but can process an input space of up to 128&lt;formula formulatype="inline"&gt; &lt;tex&gt;$~\times~$&lt;/tex&gt;&lt;/formula&gt;128 pixels. Larger pixel arrays can be directly processed by tiling arrays of chips. The chip receives and generates data in AER format, which is asynchronous and digital. However, its internal operation is based on analog low-current circuit techniques. The paper describes the architecture of the chip and circuits used for the pixels, including calibration techniques to overcome mismatch. Extensive experimental results are provided, describing pixel operation and calibration, convolution processing with and without forgetting, and high-speed recognition experiments like discriminating rotating propellers of different shape rotating at speeds of up to 5000 revolutions per second. </para>
The development of optical fibres doped with rare-earth ions (1990)

Research into rare-earth ion doping of silica based optical fibres is described and a detailed study of the fabrication process reported. Dilute solutions of rare-earth ions are employed to incorporate dopants into preforms prepared by conventional methods. Alternative core glass compositions are also studied. Parameters affecting dopant incorporation, host composition and refractive index, as well as impurity concentration are investigated.&lt;br/&gt;&lt;br/&gt;Spectroscopic fluorescence and absorption measurements are presented and provide important information for device applications. In addition, fluorescence lifetime data allow the effect of dopant concentration and host composition to be analysed. Thus, a model describing the limits of doping levels is developed. The use of rare-earth ion doped fibre in several devices, both active and passive, is assessed, with special reference to the fabrication process. In particular, the effect of host glass on the laser characteristics of Tm&lt;sup&gt;3+&lt;/sup&gt; doped fibres and of the ratio of doping levels on the behaviour of Er&lt;sup&gt;3+&lt;/sup&gt;/Yb&lt;sup&gt;3+&lt;/sup&gt; codoped fibre lasers is discussed. A practical temperature sensor based on fibre doped with low levels of rare-earth ions and a fibre filter requiring heavily doped fibre are demonstrated, with suggested design for improved performance. Finally, a novel radiation dosimeter, based on Nd&lt;sup&gt;3+&lt;/sup&gt; doped fibre, is described. Unusually, the response is found to be both rereadable and linear, even at elevated temperatures, and a model is proposed to describe the behaviour of this material.&lt;br/&gt;&lt;br/&gt;In summary, the fabrication, characterisation and applications of a wide range of rare-earth ion doped optical fibres have been investigated in detail.
Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes (2011)

Massively parallel sequencing is a useful approach for characterizing T-cell receptor diversity. However, immune receptors are extraordinarily difficult sequencing targets because any given receptor variant may be present in very low abundance and may differ legitimately by only a single nucleotide. We show that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy. At two timepoints, 1 wk apart, we isolated bulk PBMC plus naïve (CD45RA+/CD45RO-) and memory (CD45RA-/CD45RO+) T-cell subsets from a healthy donor. From T-cell receptor beta chain (TCRB) mRNA we constructed and sequenced multiple libraries to obtain a total of 1.7 billion paired sequence reads. The sequencing error rate was determined empirically and used to inform a high stringency data filtering procedure. The error filtered data yielded 1,061,522 distinct TCRB nucleotide sequences from this subject which establishes a new, directly measured, lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis. TCRB nucleotide sequences obtained from two additional donors were compared to those from the first donor and revealed limited sharing (up to 1.1%) of nucleotide sequences among donors, but substantially higher sharing (up to 14.2%) of inferred amino acid sequences. For each donor, shared amino acid sequences were encoded by a much larger diversity of nucleotide sequences than were unshared amino acid sequences. We also observed a highly statistically significant association between numbers of shared sequences and shared HLA class I alleles.
Optimal management of iron deficiency anemia due to poor dietary intake (2011)

Iron is necessary for the normal development of multiple vital processes. Iron deficiency (ID) may be caused by several diseases, even by physiological situations that increase requirements for this mineral. One of its possible causes is a poor dietary iron intake, which is infrequent in developed countries, but quite common in developing areas. In these countries, dietary ID is highly prevalent and comprises a real public health problem and a challenge for health authorities. ID, with or without anemia, can cause important symptoms that are not only physical, but can also include a decreased intellectual performance. All this, together with a high prevalence, can even have negative implications for a community's economic and social development. Treatment consists of iron supplements. Prevention of ID obviously lies in increasing the dietary intake of iron, which can be difficult in developing countries. In these regions, foods with greater iron content are scarce, and attempts are made to compensate this by fortifying staple foods with iron. The effectiveness of this strategy is endorsed by multiple studies. On the other hand, in developed countries, ID with or without anemia is nearly always associated with diseases that trigger a negative balance between iron absorption and loss. Its management will be based on the treatment of underlying diseases, as well as on oral iron supplements, although these latter are limited by their tolerance and low potency, which on occasions may compel a change to intravenous administration. Iron deficiency has a series of peculiarities in pediatric patients, in the elderly, in pregnant women, and in patients with dietary restrictions, such as celiac disease.
Transplanted Skeletal Myoblasts Can Fully Replace the Infarcted Myocardium When They Survive in the Host in Large Numbers (2003)

A large number of freshly isolated neonatal SM can survive in the host and fully replace the infarcted myocardium with reverse LV remodeling in rats with MI.
Differentiation of chronic sinus diseases by measurement of inflammatory mediators (2006)

Background: Chronic rhinosinusitis (CRS) clinically is a heterogeneous group of sinus diseases, which may cover different disease entities, or may represent a disease continuum. Studying inflammatory cells and mediators in clearly defined disease subgroups may lead to a better differentiation of chronic sinus diseases. Methods: Sinonasal mucosal tissue from 10 nasal polyp (NP) patients, 13 cystic fibrosis patients (CF‐NP), eight CRS subjects without polyps, and nine control patients were stained for CD3, CD25, CD68, CD20, myeloperoxidase (MPO), CD138 and tissue homogenates were assayed for eotaxin, interleukin (IL)‐1 β , IL‐2sR α , IL‐5, interferon (IFN)‐ γ , IL‐8, transforming growth factor (TGF)‐ β 1, tumor necrosis factor‐ α , and MPO by enzyme‐linked immunosorbent assay or UNICAP system. Results: Nasal polyp and CF‐NP showed increased numbers and activation of T cells, while only NP displayed an increase in plasma cells. Nasal polyp had significantly higher levels of eosinophilic markers [eosinophils, eotaxin, and eosinophil cationic protein (ECP)] compared with CRS, controls and CF‐NP. Chronic rhinosinusitis was characterized by a Th1 polarization with high levels of IFN‐ γ and TGF‐ β , while NP showed a Th2 polarization with high IL‐5 and immunoglobulin (Ig) E concentrations. Nasal polyp and CF‐NP were discriminated by edema from CRS and controls, with CF‐NP displaying a very prominent neutrophilic inflammation. Conclusion: Based on cellular and mediator profiles, we suggest that CRS, NP, and CF‐NP are distinct disease entities within the group of chronic sinus diseases.
Multipotent stromal cells from human marrow home to and promote repair of pancreatic islets and renal glomeruli in diabetic NOD/ scid mice (2006)

We tested the hypothesis that multipotent stromal cells from human bone marrow (hMSCs) can provide a potential therapy for human diabetes mellitus. Severe but nonlethal hyperglycemia was produced in NOD/scid mice with daily low doses of streptozotocin on days 1-4, and hMSCs were delivered via intracardiac infusion on days 10 and 17. The hMSCs lowered blood glucose levels in the diabetic mice on day 32 relative to untreated controls (18.34 mM +/- 1.12 SE vs. 27.78 mM +/- 2.45 SE, P = 0.0019). ELISAs demonstrated that blood levels of mouse insulin were higher in the hMSC-treated as compared with untreated diabetic mice, but human insulin was not detected. PCR assays detected human Alu sequences in DNA in pancreas and kidney on day 17 or 32 but not in other tissues, except heart, into which the cells were infused. In the hMSC-treated diabetic mice, there was an increase in pancreatic islets and beta cells producing mouse insulin. Rare islets contained human cells that colabeled for human insulin or PDX-1. Most of the beta cells in the islets were mouse cells that expressed mouse insulin. In kidneys of hMSC-treated diabetic mice, human cells were found in the glomeruli. There was a decrease in mesangial thickening and a decrease in macrophage infiltration. A few of the human cells appeared to differentiate into glomerular endothelial cells. Therefore, the results raised the possibility that hMSCs may be useful in enhancing insulin secretion and perhaps improving the renal lesions that develop in patients with diabetes mellitus.
Development of Virtual Navigation in Skull Base Surgery (2008)

Objective: A virtual navigation system consists of a three-dimensional (3D) image and navigation system. The virtual navigation is developed and applied to clinical cases in skull base surgery.
Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10 (2009)

Monoclonal antibodies b12 and 4E10 are broadly neutralizing against a variety of strains of the human immunodeficiency virus type 1 (HIV-1). The epitope for b12 maps to the CD4-binding site in the gp120 subunit of HIV-1's trimeric gp120-gp41 envelope spike, whereas 4E10 recognizes the membrane-proximal external region (MPER) of gp41. Here, we constructed and compared a series of architectures for the b12 and 4E10 combining sites that differed in size, valency, and flexibility. In a comparative analysis of the ability of the b12 and 4E10 constructs to neutralize a panel of clade B HIV-1 strains, we observed that the ability of bivalent constructs to cross-link envelope spikes on the virion surface made a greater contribution to neutralization by b12 than by 4E10. Increased distance and flexibility between antibody combining sites correlated with enhanced neutralization for both antibodies, suggesting restricted mobility for the trimeric spikes embedded in the virion surface. The size of a construct did not appear to be correlated with neutralization potency for b12, but larger 4E10 constructs exhibited a steric occlusion effect, which we interpret as evidence for restricted access to its gp41 epitope. The combination of limited avidity and steric occlusion suggests a mechanism for evading neutralization by antibodies that target epitopes in the highly conserved MPER of gp41.
Prevention of Central Venous Catheter-Related Bloodstream Infection by Use of an Antiseptic-Impregnated Catheter (1997)

The chlorhexidine-silver sulfadiazine catheter is well tolerated, reduces the incidence of catheter-related infection, extends the time that noncuffed central venous catheters can be safely left in place for the short term, and should allow cost savings.
Rasch Analysis of the Activities-Specific Balance Confidence Scale in Older Adults Seeking Outpatient Rehabilitation Services (2018)

Background The Activities-specific Balance Confidence (ABC) scale measures confidence in performing various ambulatory activities without falling or experiencing a sense of unsteadiness. Objectives This study (1) examined the ABC scale (0-100) using Rasch analysis, (2) assessed statistically reliable change, and (3) developed a functional staging to guide clinical interpretation of a patient's improvement. Methods The authors examined rating-scale structure, item difficulty hierarchy, item fit, person-item match, separation index, differential item functioning, test precision, and unidimensionality. Additionally, this cross-sectional study of 5012 older patients seeking outpatient rehabilitation therapy in 123 clinics estimated the minimal detectable change and developed a functional staging. Results The item "walk outside on icy sidewalks" was the most difficult item, while the item "reach for a small can off a shelf at eye level" was the easiest item. Overall, average patient ability estimates of 56.2 ± 20.3 were slightly higher than the average item difficulty estimates of 45.9 ± 7.8. With a separation index equal to 3.65, the ABC scale items can differentiate individuals into 5.2 statistically distinct strata. Most ABC scale items were free of differential item functioning. For example, "walk outside on icy sidewalks" was easier for patients who were underweight. Results supported unidimensionality of the ABC scale, with the first factor explaining 77% of the total variance. The estimated minimal detectable change was 15 points. The authors provided an example of functional staging application. Conclusion Results supported sound psychometric properties and clinical usage of the ABC scale for older adults seeking outpatient rehabilitation therapy. J Orthop Sports Phys Ther 2018;48(7):574-583. Epub 30 Mar 2018. doi:10.2519/jospt.2018.8023.