gebhart/patrepeval huggingface dataset:
Statistical tests of neutrality of mutations. (1993)

Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occurred in the external branches and internal mutations are mutations that occurred in the internal branches of the genealogy. Under the assumption of selective neutrality, the expected number of external mutations is equal to theta = 4Ne mu, where Ne is the effective population size and mu is the rate of mutation per gene per generation. Interestingly, this expectation is independent of the sample size. The number of external mutations is likely to deviate from its neutral expectation when there is selection while the number of internal mutations is less affected by the presence of selection. Statistical properties of the numbers of external mutations and of internal mutations are studied and their relationships to two commonly used estimates of theta are derived. From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.
The CXCR4 antagonist plerixafor corrects panleukopenia in patients with WHIM syndrome (2011)

WHIM syndrome is a rare congenital immunodeficiency disorder characterized by warts, hypogammaglobulinemia, infections, and myelokathexis (neutropenia because of impaired egress from the BM); most patients also have severe panleukopenia. Because WHIM syndrome is caused by mutations in the chemokine receptor CXCR4 that result in increased agonist-dependent signaling, we hypothesized that the CXCR4 antagonist plerixafor (Mozobil [Genyzme Corporation], AMD3100), might be an effective treatment. To test this, we enrolled 3 unrelated adult patients with the most common WHIM mutation, CXCR4(R334X), in a phase 1 dose-escalation study. Plerixafor increased absolute lymphocyte, monocyte, and neutrophil counts in blood to normal without significant side effects in all 3 patients. Peak responses occurred at 3-12 hours after injection and waned by 24 hours after injection which tracked the drug's pharmacokinetics. All 3 cell types increased in a dose-dependent manner with the rank order of responsiveness absolute lymphocyte > monocyte > neutrophil. These data provide the first pharmacologic evidence that panleukopenia in WHIM syndrome is caused by CXCL12-CXCR4 signaling-dependent leukocyte sequestration, and support continued study of plerixafor as mechanism-based therapy in this disease. This study is registered at http://www.clinicaltrials.gov as NCT00967785.
BACTERIAS PROMOTORAS DEL CRECIMIENTO VEGETAL EN EL CULTIVO DEL ARROZ (Oryza sativa L.). PERSPECTIVAS DE SU USO EN CUBA (2007)

"Rice is one of the most important food and work supplies worldwide, besides that it is highly consumed. As a sustainable agriculture strategy, crop yield increments have been encouraged through combining chemical fertilizers and biofertilizers adequately. In this sense, the application of microbial inoculants has been proved as an ecological alternative to preserve the environment and ecosystem. The Plant Growth Promoting Bacteria (PGPB) are among the main groups of microorganisms used with this purpose, due to their abilities of interacting with plants through different mechanisms of action, such as phytohormone production, biological nitrogen fixation and pathogen biocontrol. The aim of this work was to review the importance of employing PGPB, dealing with some relevant subjects, such as their isolation and identification methods, as well as their main mechanisms of action, showing their potential to be used in an essential crop like rice."
A randomized, double-blind, placebo-controlled multicentre study to evaluate the efficacy and safety of diclofenac 4% spray gel in the treatment of acute uncomplicated ankle sprain (2013)

Diclofenac 4% spray gel rapidly relieves pain and improves mobility in patients with acute, uncomplicated ankle sprain and is well tolerated. It may be a useful treatment option for other acute soft tissue injuries.
High efficiency grating coupler between silicon-on-insulator waveguides and perfectly vertical optical fibers (2007)

A high-efficiency waveguide-to-fiber grating coupler for silicon-on-insulator waveguides was designed. Perfectly vertical fiber coupling is achieved by using an asymmetric grating structure to suppress the second-order Bragg reflection from the grating. The ability to use a perfectly vertical positioned optical fiber simplifies the packaging of the photonic integrated circuit. A coupling efficiency of 80% at a wavelength of 1.55 microm is obtained.
Tunable Disassembly of Micelles Using a Redox Trigger (2007)

A simple design for stimuli-responsive micellar disassembly has been demonstrated on the basis of a surfactant molecule wherein the hydrophilic head group is connected to the hydrophobic tail through a redox-sensitive disulfide linker. The disassembly kinetics is tuned by mixing the stimuli-responsive surfactant with a suitable nonresponsive co-surfactant in various ratios, which helps in gaining control over the release rate of encapsulated dye molecules from such mixed micelles.
Third Generation WCDMA Radio Evolution (2006)

3rd Generation Partner Ship Project (3GPP) produced the first full version of the Wideband CDMA (WCDMA) standard at the end of 1999. Release’99, meets all the IMT-2000 requirements, including 2 Mbps data rate with variable bit rate capability, support of multi-service, quality of service differentiation and efficient packet data. The Release’5 specifications were created in March 2002 and they contain downlink packet data operation enhancement, under the title High Speed Downlink Packet Access (HSDPA). HSDPA utilizes Hybrid Automatic Repeat Request (HARQ), link adaptation and higher order modulation for improving data spectral efficiency and for pushing bit rates beyond 10 Mbps. The further 3GPP releases will study the enhancements of packet data performance in uplink. Other important features in future 3GPP releases include advanced antenna technologies and WCDMA standard for new spectrum allocations. The paper describes the main solutions of 3GPP WCDMA standard in more detail.
Chitosan Membranes for Reverse Osmosis Application (1984)

Alkali resistant reverse osmosis membranes were fabricated by spreading solutions of chitosan, a poly-N-acetyl glucosamine, in 2.0% acetic acid on a glass plate. The membrane had a flux rate of 1.67 ± 10-3 cm3/cm2/sec and a salt rejection capability of 78.8% with 0.2% NaCl at 680 psi. Addition of 40% polyethylene glycol to the membrane casting solution increased permeability, while 10% chloromethyl oxirane improved durability of the membranes.
An inducible arylsulfatase of Volvox carteri with properties suitable for a reporter‐gene system (1994)

The multicellular green flagellate Volvox carteri synthesizes a periplasmic arylsulfatase in response to sulfur deprivation. The inducible enzyme has been purified to homogeneity and characterized. The corresponding gene and cDNA have been cloned. Determination of the sequence of genomic clones and comparisons to the cDNA sequence, revealed sixteen introns and seventeen exons that encode a 649-amino-acid polypeptide chain. Since the arylsulfatase enzyme is readily assayed using chromogenic substrates, but is not detectable in cells grown in sulfate-containing medium, the gene encoding arylsulfatase may be useful as a reporter gene in V. carteri. In addition, the highly regulated promoter of the arylsulfatase gene suggests its suitability as a tool for producing inducible expression vectors for cloned genes.
Sensitivity of Digital Thermal Monitoring Parameters to Reactive Hyperemia (2010)

Both structural and functional evaluations of the endothelium exist in order to diagnose cardiovascular disease (CVD) in its asymptomatic stages. Vascular reactivity, a functional evaluation of the endothelium in response to factors such as occlusion, cold, and stress, in addition to plasma markers, is the most widely accepted test and has been found to be a better predictor of the health of the endothelium than structural assessment tools such as coronary calcium scores or carotid intima-media thickness. Among the vascular reactivity assessment techniques available, digital thermal monitoring (DTM) is a noninvasive technique that measures the recovery of fingertip temperature after 2-5 min of brachial occlusion. On release of occlusion, the finger temperature responds to the amount of blood flow rate overshoot referred to as reactive hyperemia (RH), which has been shown to correlate with vascular health. Recent clinical trials have confirmed the potential importance of DTM as an early stage predictor of CVD. Numerical simulations of a finger were carried out to establish the relationship between DTM and RH. The model finger consisted of essential components including bone, tissue, major blood vessels (macrovasculature), skin, and microvasculature. The macrovasculature was represented by a pair of arteries and veins, while the microvasculature was represented by a porous medium. The time-dependent Navier-Stokes and energy equations were numerically solved to describe the temperature distribution in and around the finger. The blood flow waveform postocclusion, an input to the numerical model, was modeled as an instantaneous overshoot in flow rate (RH) followed by an exponential decay back to baseline flow rate. Simulation results were similar to clinically measured fingertip temperature profiles in terms of basic shape, temperature variations, and time delays at time scales associated with both heat conduction and blood perfusion. The DTM parameters currently in clinical use were evaluated and their sensitivity to RH was established. Among the parameters presented, temperature rebound (TR) was shown to have the best correlation with the level of RH with good sensitivity for the range of flow rates studied. It was shown that both TR and the equilibrium start temperature (representing the baseline flow rate) are necessary to identify the amount of RH and, thus, to establish criteria for predicting the state of specific patient's cardiovascular health.
THE BROMINOLYSIS OF CARBOHYDRATE IODIDES: I. ACETYLATED 6-DEOXY-6-IODO AND 2-DEOXY-2-IODO GLYCOSIDES (1964)

Reaction of methyl 6-deoxy-6-iodo-α-D-glucopyranoside triacetate with an excess of bromine in glacial acetic acid; N in potassium acetate, gave a 1.1:1 mixture of the products resulting from replacement of the iodine by bromine and by acetoxy group, respectively. When 2 moles of silver acetate were present per mole of bromine, the reaction was much more rapid and only methyl α-D-glucopyranoside tetraacetate was formed. The brominolysis of methyl 2-deoxy-2-iodo-α-D-mannopyranoside triacetate proceeded at a useful rate only when catalyzed by silver acetate. The main product of the reaction appeared to be methyl 3-acetoxy-2-bromo-2-deoxy-α-D-arabino-hexopyranoside triacetate. The compound could be converted by way of sodium borohydride reduction to methyl 2-bromo-2-deoxy-α-D-altropyranoside and by way of zinc dust reduction to methyl 2-deoxy-α-D-erythro-hexopyranoside-3-ulose diacetate. About 20% of the reaction proceeded with migration of the methoxy group to the 2-position to yield 2-O-methyl-D-glucose tetraacetate. The mechanisms of these reactions are discussed.
High Levels of Neutralizing Autoantibodies Against IL‐1α are Associated with a Better Prognosis in Chronic Polyarthritis: a Follow‐Up Study (1997)

Neutralizing autoantibodies to interleukin (IL)-1 alpha were detected in a subset of chronic polyarthritis patients characterized by an increased proportion of patients with primary Sjögren's syndrome or self-limiting inflammatory arthritis, diseases with a much better prognosis than rheumatoid arthritis (RA). The evolution of anti-IL-1 alpha antibody levels was followed over 3 years. Incidence and levels were higher in patients with a benign form of polyarthritis. In these patients levels remained stable or increased over the follow-up period. In contrast, incidence and levels were lower and some RA patients became negative. Negative correlations were observed between the levels of anti-IL-1 alpha antibodies and the clinical and biological indices of disease activity. The relative risk factor of developing RA was 12 in the absence of high anti-IL-1 alpha antibody levels and 18.2 when associated with the presence of HLA-DR4. In conclusion, the presence of anti-IL-1 alpha autoantibodies appears to be protective and their detection could represent a marker of good prognosis for destruction.
Mutational analysis of N-linked glycosylation sites of Friend murine leukemia virus envelope protein (1991)

The roles played by the N-linked glycans of the Friend murine leukemia virus envelope proteins were investigated by site-specific mutagenesis. The surface protein gp70 has eight potential attachment sites for N-linked glycan; each signal asparagine was converted to aspartate, and mutant viruses were tested for the ability to grow in NIH 3T3 fibroblasts. Seven of the mutations did not affect virus infectivity, whereas mutation of the fourth glycosylation signal from the amino terminus (gs4) resulted in a noninfectious phenotype. Characterization of mutant gene products by radioimmunoprecipitation confirmed that glycosylation occurs at all eight consensus signals in gp70 and that gs2 carries an endoglycosidase H-sensitive glycan. Elimination of gs2 did not cause retention of an endoglycosidase H-sensitive glycan at a different site, demonstrating that this structure does not play an essential role in envelope protein function. The gs3- mutation affected a second posttranslational modification of unknown type, which was manifested as production of gp70 that remained smaller than wild-type gp70 after removal of all N-linked glycans by peptide N-glycosidase F. The gs4- mutation decreased processing of gPr80 to gPr90, completely inhibited proteolytic processing of gPr90 to gp70 and Pr15(E), and prevented incorporation of envelope products into virus particles. Brefeldin A-induced mixing of the endoplasmic reticulum and parts of the Golgi apparatus allowed proteolytic processing of wild-type gPr90 to occur in the absence of protein transport, but it did not overcome the cleavage defect of the gs4- precursor, indicating that gs4- gPr90 is resistant to the processing protease. The work reported here demonstrates that the gs4 region is important for env precursor processing and suggests that gs4 may be a critical target in the disruption of murine leukemia virus env product processing by inhibitors of N-linked glycosylation.
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018)

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.
The role of endogenous gibberellins during fruit and seed development: Studies on gibberellin‐deficient genotypes of Arabidopsis thaliana (1986)

Siliqua development was studied in the wild type line Landsberg erecta and the GA‐sensitive mutant ga‐1 of Arabidopsis thaliana (L.) Heynh. Reciprocal crosses between wild type and ga‐l mutant, and self pollinations of either parent have shown that siliqua growth is determined by endogenous GAs originating from maternal tissues and embryo. The ga‐1 mutant either self pollinated or cross‐pollinated with wild type pollen showed reduced siliqua growth, which to a large extent could be overcome by exogenously applied GAs. The siliquae of the ga‐1 mutant possessed very reduced ent ‐kaurene synthesizing capacity and no detectable endogenous GA‐activity indicating an early block in the GA‐biosynthetic pathway. Seed weight is not affected by GA‐deficiency during development.
Irinotecan Plus Fluorouracil/Leucovorin for Metastatic Colorectal Cancer: A New Survival Standard (2001)

The combination of irinotecan/5-FU/LV is superior to 5-FU/LV alone as first-line therapy for patients with metastatic colorectal cancer, offering consistently improved tumor control and prolonged survival. Irinotecan-based combination therapy sets a new survival standard for the treatment of this life-threatening disease.
Neuronal Loss Is Greater in the Locus Coeruleus Than Nucleus Basalis and Substantia Nigra in Alzheimer and Parkinson Diseases (2003)

For both AD and PD the greatest neuronal loss was found in the LC. In AD, neuronal loss was most severe and best correlated with the duration of illness in the LC, rather than in NB as traditionally expected. Correlations between neuronal loss in the LC and NB (but not SN) in both PD and AD suggest that the former 2 nuclei may share common pathogenetic susceptibilities. Given the prominent loss of neurons in the LC, detection and treatment of noradrenergic deficiencies warrant attention in both AD and PD.
Shedding of syncytiotrophoblast microvilli into the maternal circulation in pre‐eclamptic pregnancies (1998)

STBM are shed into the maternal circulation (microvillous deportation) and are present in significantly increased amounts in pre-eclamptic women. They may contribute to the endothelial dysfunction underlying the maternal syndrome of pre-eclampsia.
The regulation of integrin function by divalent cations (2012)

Integrins are a family of α/β heterodimeric adhesion metalloprotein receptors and their functions are highly dependent on and regulated by different divalent cations. Recently advanced studies have revolutionized our perception of integrin metal ion-binding sites and their specific functions. Ligand binding to integrins is bridged by a divalent cation bound at the MIDAS motif on top of either α I domain in I domain-containing integrins or β I domain in α I domain-less integrins. The MIDAS motif in β I domain is flanked by ADMIDAS and SyMBS, the other two crucial metal ion binding sites playing pivotal roles in the regulation of integrin affinity and bidirectional signaling across the plasma membrane. The β-propeller domain of α subunit contains three or four β-hairpin loop-like Ca(2+)-binding motifs that have essential roles in integrin biogenesis. The function of another Ca(2+)-binding motif located at the genu of α subunit remains elusive. Here, we provide an overview of the integrin metal ion-binding sites and discuss their roles in the regulation of integrin functions.
Impedance matched channel walls in acoustofluidic systems (2013)

Acoustophoresis in bulk acoustic wave (BAW) devices typically operates with an ultrasonic standing wave in a microfluidic channel between two opposing silicon walls, which act as both the acoustic and the fluidic boundary. In this paper, we describe BAW devices with an additional material layer of polydimethylsiloxane (PDMS). This PDMS wall is introduced to decouple the acoustic boundary (silicon wall) from the fluidic boundary (PDMS wall) by acoustic impedance matching. The acoustic field and the resulting particle manipulation are thereby less restricted than in conventional BAW devices. In the presented devices, particle accumulation lines can be placed arbitrarily within the fluidic domain, which strongly increases the possibility of acoustophoresis. The paper covers experimental results, an analytical model in good agreement and microfabrication techniques for PDMS enclosed in a microchannel. An application example for microparticle concentration is demonstrated. The presented approach offers further potential for biotechnological applications such as particle separation, enhanced particle sensors and cell handling.
Evolutionarily conserved gene family important for fat storage (2007)

The ability to store fat in the form of cytoplasmic triglyceride droplets is conserved from Saccharomyces cerevisiae to humans. Although much is known regarding the composition and catabolism of lipid droplets, the molecular components necessary for the biogenesis of lipid droplets have remained obscure. Here we report the characterization of a conserved gene family important for lipid droplet formation named fat-inducing transcript (FIT). FIT1 and FIT2 are endoplasmic reticulum resident membrane proteins that induce lipid droplet accumulation in cell culture and when expressed in mouse liver. shRNA silencing of FIT2 in 3T3-LI adipocytes prevents accumulation of lipid droplets, and depletion of FIT2 in zebrafish blocks diet-induced accumulation of lipid droplets in the intestine and liver, highlighting an important role for FIT2 in lipid droplet formation in vivo. Together these studies identify and characterize a conserved gene family that is important in the fundamental process of storing fat.
Vibrational Spectroscopy and Mass Spectrometry for Characterization of Soft Landed Polyatomic Molecules (2011)

We report implementation of two powerful characterization tools, in situ secondary ion mass spectrometry (SIMS) and ex situ surface enhanced Raman spectroscopy (SERS), in analyzing surfaces modified by ion soft landing (SL). Cations derived from Rhodamine 6G are soft landed onto Raman-active silver colloidal substrates and detected using SERS. Alternatively and more conveniently, high-quality SERS data are obtained by spin coating a silver colloidal solution over the modified surface once SL is complete. Well-defined SERS features are observed for Rhodamine 6G in as little as 15 min of ion deposition. Deposition of ~3 pmo1 gave high-quality SERS spectra with characteristic spectroscopic responses being derived from just ~0.5 fmol of material. Confocal SERS imaging allowed the enhancement to be followed in different parts of deposited dried droplets on surfaces. Characteristic changes in Raman spectral features occur when Rhodamine 6G is deposited under conditions that favor gas-phase ion fragmentation. Simultaneous deposition of both the intact dye and its fragment ion occurs and is confirmed by SIMS analysis. The study was extended to other Raman active surfaces, including Au nanostar and Au coated Ni nanocarpet surfaces and to SL of other molecules including fluorescein and methyl red. Overall, the results suggest that combination of SERS and SIMS measurements are effective in the characterization of surfaces produced by ion SL with significantly enhanced molecular specificity.
A second-generation anthrax "smoke detector" (2004)

We have demonstrated quantification of aerosolized bacterial spores with a response time of 10 minutes, a sensitivity of 50 spores per liter of air, and a dynamic range of 4 orders of magnitude using a bioaerosol sampler, thermal spore lysis, and a lifetime-gated fluorimeter. This technology is amenable to complete automation and enables long-term, unattended monitoring for airborne bacterial spores. The anthrax spore detector (ASD) technology is envisioned to serve as a front-end monitor that promises tremendous reduction in operating costs for anthrax monitoring at the U.S. Postal Service.