gebhart/patrepeval huggingface dataset:
Development of a Phage Cocktail to Control Proteus mirabilis Catheter-associated Urinary Tract Infections (2016)

Proteus mirabilis is an enterobacterium that causes catheter-associated urinary tract infections (CAUTIs) due to its ability to colonize and form crystalline biofilms on the catheters surface. CAUTIs are very difficult to treat, since biofilm structures are highly tolerant to antibiotics. Phages have been used widely to control a diversity of bacterial species, however, a limited number of phages for P. mirabilis have been isolated and studied. Here we report the isolation of two novel virulent phages, the podovirus vB_PmiP_5460 and the myovirus vB_PmiM_5461, which are able to target, respectively, 16 of the 26 and all the Proteus strains tested in this study. Both phages have been characterized thoroughly and sequencing data revealed no traces of genes associated with lysogeny. To further evaluate the phages' ability to prevent catheter's colonization by Proteus, the phages adherence to silicone surfaces was assessed. Further tests in phage-coated catheters using a dynamic biofilm model simulating CAUTIs, have shown a significant reduction of P. mirabilis biofilm formation up to 168 h of catheterization. These results highlight the potential usefulness of the two isolated phages for the prevention of surface colonization by this bacterium.
Understanding the role of von Willebrand factor and its cleaving protease ADAM TS13 in the pathophysiology of critical illness* (2007)

Pediatric Critical Care Medicine 8(2):p 187-189, March 2007. | DOI: 10.1097/01.CCM.0000257468.75474.D4
Thin strained layers inserted in compositionally graded SiGe buffers and their effects on strain relaxation and dislocation (2007)

The effect of inserting compressively or tensely strained layers into compositionally graded SiGe buffers on strain relaxation and threading dislocation density (TDD) was investigated. The samples having compressively strained layers showed lower TDD and more enhanced relaxation than those having tensely strained layers. In addition, dislocations were accumulated at the top part of the tensely strained layers within the graded buffers, while no accumulation was found at the compressively strained layers. These results might be due to the effect of strain from the thin inserted layers on the dislocation interactions in the compressively strained graded buffers.
Capillary electrophoresis-atmospheric pressure ionization mass spectrometry for the characterization of peptides (1991)

On-line capillary electrophoresis (CE) separations are shown for a synthetic peptide mixture and a tryptic digest of human hemoglobin in an uncoated fused-silica capillary with detection using atmospheric pressure ionization mass spectrometry (API-MS). The CE system utilized a 1-m capillary column of either 75- or 100-microns I.D. These somewhat larger inside diameters allow higher sample capacities for MS detection and the 1-m length facilitates connecting the CE column to the liquid junction-ion spray interface and MS system. Low volatile buffer concentrations (15-20 mM) of ammonium acetate or ammonium formate, and high organic modifier content (5-50%) of methanol or acetonitrile facilitates ionization under electrospray conditions. This study shows that peptides separated by CE may be transferred to the API-MS system through a liquid junction coupling to the pneumatically assisted electrospray (ion spray) interface at low buffer pH when the electroosmotic flow is low (0-0.04 microliter/min). CE-MS as described herein is facilitated by features in modern CE instrumentation including robotic cleaning and pressurization of the capillary inlet. The latter is particularly useful for repetitive rinsing and conditioning of the capillary column between analyses in addition to continuous 'infusion' of sample to the mass spectrometer for tuning purposes. In addition to facile molecular weight determination, amino acid sequence information for peptides may be obtained by utilizing on-line tandem MS. After the tryptic digest sample components enter the API-MS system, the molecular ion species of individual peptides may be focussed and transmitted into the collision cell of the tandem triple quadrupole mass spectrometer. Collision-induced dissociation of protonated peptide molecules yielded structural information for their characterization following injection of 10 pmol of a tryptic digest from human hemoglobin.
Phase Variation of Type 1 Fimbriae in <i>Escherichia coli</i> Is Under Transcriptional Control (1981)

An operon fusion of the lac genes to those required for synthesis of type 1 fimbriae (pili) has been achieved in a K12 strain of Escherichia coli lysogenized by the bacteriophage mu d (Ap4, lac). Synthesis of beta-galactosidase, therefore, reflected pil gene transcription and was used as a probe of fimbrial regulation. Expression of the operon fusion was found to oscillate, demonstrating that phase variation between fimbriate and nonfimbriate states is under transcriptional control. The transition rates from fimbriate to nonfimbriate were 1.05 X 10(-3) per bacterium per generation and from nonfimbriate to fimbriate, 3.12 X 10(-3) per bacterium per generation.
Misfolded Proteins Traffic from the Endoplasmic Reticulum (ER) Due to ER Export Signals (2006)

Most misfolded secretory proteins remain in the endoplasmic reticulum (ER) and are degraded by ER-associated degradation (ERAD). However, some misfolded proteins exit the ER and traffic to the Golgi before degradation. Using model misfolded substrates, with or without defined ER exit signals, we found misfolded proteins can depart the ER by continuing to exhibit the functional export signals present in the corresponding correctly folded proteins. Anterograde transport of misfolded proteins utilizes the same machinery responsible for exporting correctly folded proteins. Passive ER retention, in which misfolded proteins fail to exit the ER due to the absence of exit signals or the inability to functionally present them, likely contributes to the retention of nonnative proteins in the ER. Intriguingly, compromising ERAD resulted in increased anterograde trafficking of a misfolded protein with an ER exit signal, suggesting that ERAD and ER exit machinery can compete for binding of misfolded proteins. Disabling ERAD did not result in transport of an ERAD substrate lacking an export signal. This is an important distinction for those seeking possible therapeutic approaches involving inactivating ERAD in anticipation of exporting a partially active protein.
AxFTL: Exploiting Error Tolerance for Extending Lifetime of NAND Flash Storage (2020)

NAND flash storage has become a standard choice in consumer electronics and is gaining popularity in enterprise systems due to its superior performance and low-power consumption. While its cost disadvantage is rapidly fading thanks to multibit cell technologies and 3-D stacking architectures, the challenge of limited endurance is still lingering and is expected to become more daunting as bits-per-cell continues to increase. In this article, we propose a novel flash translation layer (FTL) design named AxFTL (Approximate FTL) that extends the lifetime of NAND flash storage for error-tolerant applications. For error-tolerant data, AxFTL adopts shallow erase that lowers erase voltage to reduce the erase-induced wearing at the cost of an increased error rate. AxFTL manages multiple groups of blocks by error rates and allocates them according to the error tolerance of write requests. The key components of AxFTL include error tolerance-aware garbage collection and wear leveling schemes that manage the blocks with different error rates with minimal overhead. We implement AxFTL in an SSD simulator for the evaluation of the lifetime improvement and the actual allocation of the blocks. For application-level evaluation, we apply AxFTL to compressed video storage and evaluate the quality of video playback. Our experimental results show that AxFTL greatly improves the lifetime of NAND flash storage by 61% while maintaining a high structural similarity (SSIM) of 0.86 as compared to the conventional FTL.
Internet advertising: Is anybody watching? (2003)

Click-through rates are still the de facto measure of Internet advertising effectiveness. Unfortunately, click-through rates have plummeted. This decline prompts two critical questions: (1) Why do banner ads seem to be ineffective and (2) what can advertisers do to improve their effectiveness? To address these questions, we utilized an eye-tracking device to investigate online surfers’ attention to online advertising. Then we conducted a large-scale survey of Internet users’ recall, recognition, and awareness of banner advertising. Our research suggests that the reason why click-through rates are low is that surfers actually avoid looking at banner ads during their online activities. This implies that the larger part of a surfer's processing of banners will probably be done at the pre-attentive level. If such is the case, click-through rate is an ineffective measure of banner ad performance. Our research also shows that banner ads do have an impact on traditional memory-based measure of effectiveness. Thus, we claim that advertisers should rely more on traditional brand equity measures such as brand awareness and advertising recall. Using such measures, we show that repetition affects unaided advertising recall, brand recognition, and brand awareness and that a banner's message influences both aided advertising recall and brand recognition.
Depressed immunity and impaired proliferation of hematopoietic progenitor cells in patients with complete spinal cord injury (2000)

The bone marrow is supplied with both sensory and autonomic neurons, but their roles in regulating hematopoietic and immunocompetent cells are unknown. Leukocyte growth and activity in patients with stable and complete spinal cord injuries were studied. The innervation of the bone marrow below the injury level lacked normal supraspinal activity, that is, a decentralized bone marrow. Lymphocyte functions were markedly decreased in injured patients. Long-term colony formation of all hematopoietic cell lineages, including dendritic cells, by decentralized bone marrow cells was substantially reduced. It was concluded that nonspecific and adaptive lymphocyte-mediated immunity and growth of early hematopoietic progenitor cells are impaired in patients with spinal cord injuries. Possibly, this reflects cellular defects caused by the malfunctioning neuronal regulation of immune and bone marrow function.
<i>p53</i> and K-<i>ras</i> Gene Mutations Correlate With Tumor Aggressiveness But Are Not of Routine Prognostic Value in Colorectal Cancer (1999)

p53 mutations alone or in combination with K-ras mutations are correlated with a worse outcome. However, the routine use of these mutations as prognostic markers in the clinical setting is not recommended.
Parasitic Layer-Based Radiation Pattern Reconfigurable Antenna for 5G Communications (2017)

The design, prototyping, and characterization of a radiation pattern reconfigurable antenna (RA) targeting 5G communications are presented. The RA is based on a reconfigurable parasitic layer technique in which a driven dipole antenna is located along the central axis of a 3-D parasitic layer structure enclosing it. The reconfigurable parasitic structure is similar to a hexagonal prism, where the top/bottom bases are formed by a hexagonal domed structure. The surfaces of the parasitic structure house electrically small metallic pixels with various geometries. The adjacent pixels are connected by PIN diode switches to change the geometry of the parasitic surface, thus providing reconfigurability in the radiation pattern. This RA is designed to operate over a 4.8–5.2 GHz frequency band, producing various radiation patterns with a beam-steering capability in both the azimuth ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$0 {^{\circ }} <\phi < 360 {^{\circ }}$ </tex-math></inline-formula> ) and elevation planes ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$-18 {^{\circ }} <\theta < 18 {^{\circ }}$ </tex-math></inline-formula> ). Small-cell access points equipped with RAs are used to investigate the system level performances for 5G heterogeneous networks. The results show that using distributed mode optimization, RA equipped small-cell systems could provide up to 29% capacity gains and 13% coverage improvements as compared to legacy omnidirectional antenna equipped systems.
Anti-inflammatory Sesquiterpene-quinones from the New Zealand Sponge <i>Dysidea</i> cf. <i>c</i><i>ristagalli</i> (2005)

The inhibition of superoxide production by human neutrophils has been used to screen New Zealand's unique biota for anti-inflammatory natural products. Bioactivity-directed isolation on an extract of the sponge Dysidea cf. cristagalli led to a new sesquiterpene-quinone (4) with anti-inflammatory activity, plus acetylated hydroquinone (3). These compounds inhibited superoxide production in vitro with IC50's of 3 microM (3) and 11 microM (4).
Theory of the Concave Grating III Seya-Namioka Monochromator*†‡ (1959)

As an example of a mounting in which the optical components are not on the Rowland cylinder, the Seya-Namioka mounting is treated mainly from the standpoint of physical optics. An ambiguity in the physical meaning of Beutler’s focal conditions is clarified; using the corrected condition a brief summary of the optical conditions in this mounting is given. Astigmatism, spectral line shape, instrumental resolving power, and optimum grating width are discussed in detail and, for convenience of practical application, numerical results are also given for the following conditions: 1-m concave grating with 15 000 lines/in., first order spectrum, with ratios of the radius of curvature of the grating to the distances between the grating center and the entrance and exit slits 1.2223, and 1.2230, respectively, and the angle between the lines connecting the grating center to the entrance and exit slit 70° 15′.
The optimization of wireless power transmission: design and realization (2012)

The example validates the feasibility of the proposed method. Introduction of novel designs enables further improvement of this method.
A collagen based cryogel bioscaffold coated with nanostructured polydopamine as a platform for mesenchymal stem cell therapy (2018)

Cryo-hydrogels (cryogels) are polymer hydrogels formed at sub-zero temperatures. Bioscaffolds created from cryogels have interconnected macropores which allow for cell migration, tissue-ingrowth, unhindered diffusion of solutes and mass transport of therapeutics. In this study, we developed collagen based cryogel bioscaffolds and coated them with polydopamine using a simple two-step technique. Cryogel bioscaffolds were synthesized by collagen crosslinking at -20°C and exhibited a macroporous interconnected architecture with 75% ± 3% porosity. Two groups of pore sizes were observed: 300 ± 50 µm and 30 ± 10 µm in diameter. The addition of a polydopamine coating to cryogel bioscaffolds was confirmed using composition analysis. This resulted in a 41% ± 5% decrease in water uptake, 81% ± 10% decrease in swelling rate and 12% ± 3% decrease in their degree of dissolution (p < 0.05), with a 48% ± 2% increase in stiffness and 57% ± 5% increase in compressive strength (p < 0.05). Seeding adipose tissue-derived mesenchymal stem cells (AD-MSCs) into polydopamine coated-cryogel bioscaffolds resulted in cells demonstrating a 52% ± 4% increase in viability and 33% ± 3% increase in proliferation when compared to AD-MSCs seeded into uncoated-cryogel bioscaffolds (p < 0.05). In summary, our novel polydopamine coated-cryogel bioscaffold represents an efficient and low-cost bioscaffold platform to support MSC therapies. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2213-2228, 2018.
Polyhedral Oligomeric Silsesquioxane as a Ligand for CdSe Quantum Dots (2013)

We report the synthesis of CdSe quantum dots (QDs) using a mercapto-substituted polyhedral oligomeric silsesquioxane (SH-POSS). The bulky siloxane cage-like core of the ligand makes this an ideal steric stabilizer, and comparison with conventional branched alkyl phosphonic acid capped CdSe QDs shows SH-POSS capped QDs to have superior optical properties including photoluminescence quantum efficiencies and fluorescence lifetimes. The POSS shell allows for the access of small electrolyte ions and electron transport from the surface of the QDs, evidenced by better performance as a photosensitizer in conjunction with a titania nanotube array electron acceptor in comparison to the conventionally stabilized QDs.
Male menopause (1998)

Menopause is the cessation of menses caused by the age-associated decline in gonadal hormone secretion in women. Although men do not menstruate, they do have an age-associated decline in gonadal hormone secretion. This "male menopause" is associated with loss of libido, loss of muscle mass and various other undesirable effects. The underlying causes of decreased testosterone production in older men may include decreased hypothalamic gonadotropin releasing hormone (GnRH) secretion, impaired feedforward effect of luteinizing hormone (LH) on testosterone secretion and decreased testosterone release from the Leydig cells. When chronic illness is superimposed on healthy aging, there are further decrements in testosterone availability. Although a consensus has not been reached, various studies suggest that older men may benefit from testosterone supplementation. For example, testosterone supplementation to older men seems to cause increased muscle protein synthesis, increased muscle strength and decreased cholesterol. Nevertheless, if testosterone supplementation is provided, clinicians must be vigilant to detect adverse effects such as accelerated growth of prostate carcinoma.
Vitamin D and Myocardial Infarction (1974)

A detailed investigation was carried out into the consumption of vitamin D from different sources in patients who had suffered from myocardial infarction, angina pectoris, and degenerative joint diseases. Randomly selected controls of the same ages and sex were drawn from the Central Bureau of Statistics. The consumption was significantly higher in infarction patients. A daily intake of 30 mug may be the critical level. Student's t test for trend showed increasing probability of myocardial infarction with increasing intake of vitamin D, and more infarction patients than controls had a history of kidney stone. Long-term high consumption of vitamin D may be a precipitating cause of myocardial infarction.
Host range of <i>Exserohilum monoceras</i>, a potential bioherbicide for the control of <i>Echinochloa</i> species (1997)

Fifty-six plant species in 43 genera and 19 families, selected by using the centrifugal phylogenetic method, were screened against Exserohilum monoceras, a fungus collected in the Philippines on Echinochloa colona. Trials were performed under both optimum greenhouse conditions with supplemental 24-h dew and natural field conditions with no dew supplement. The compatibility of host–pathogen interactions was characterized by the time and level of sporulation observed on detached inoculated leaves. All Echinochloa species proved to be highly susceptible to this fungus under optimum greenhouse conditions as well as in the absence of a dew supplement. Rottboellia cochinchinensis was also highly susceptible to this pathogen regardless of the presence of a supplemental dew period. Among the crops tested, only corn seedlings were slightly infected under supplemental 24-h dew conditions, but no disease symptoms were observed on corn in the absence of a dew supplement. Sorghum and sugarcane were hypersensitive to the pathogen under supplemental 24-h dew conditions, but no infection was detected in the absence of a dew supplement. All other species tested were immune to E. monoceras. Data on sporulation on detached leaves from inoculated plants indicated that E. monoceras was weakly compatible with corn. No disease symptoms and no conidia were detected on leaves of trap plants. In the field, E. monoceras produced no symptoms on corn plants. Key words: host range, bioherbicide, Exserohilum monoceras, Echinochloa crus-galli, Echinochloa colona, Echinochloa glabrescens.
World War II Pacific island guide: a geo-military study (2002)

Foreword Introduction Geo-Military Aspects of the Pacific Theater World War II in the Pacific Chronology The Islands Selected Bibliography Index
Comparative Analysis of Gene Expression by Microarray Analysis of Male and Female Flowers of<i>Asparagus officinalis</i> (2013)

To identify rapidly a number of genes probably involved in sex determination and differentiation of the dioecious plant Asparagus officinalis, gene expression profiles in early flower development for male and female plants were investigated by microarray assay with 8,665 probes. In total, 638 male-biased and 543 female-biased genes were identified. These genes with biased-expression for male and female were involved in a variety of processes associated with molecular functions, cellular components, and biological processes, suggesting that a complex mechanism underlies the sex development of asparagus. Among the differentially expressed genes involved in the reproductive process, a number of genes associated with floral development were identified. Reverse transcription-PCR was performed for validation, and the results were largely consistent with those obtained by microarray analysis. The findings of this study might contribute to understanding of the molecular mechanisms of sex determination and differentiation in dioecious asparagus and provide a foundation for further studies of this plant.
Effect of short glass fibers on the polymerization shrinkage stress of dental composite (2016)

This study examines contraction stresses of seven short fiber reinforced composites (sFRC) exhibiting different volume loads and aspect ratios (AR)* of fibres. The shift towards a greater utilization of posterior resin composites in dentistry has seen increased interest in the use of randomly oriented short glass fibers in these restorative materials. While the effect of these fibers on modulus, strength, and toughness has been studied, very little information exists on their effect on polymerization shrinkage and even less on shrinkage stress. S2-glass fibers with an average AR of 68 were used to form three experimental groups with 5%, 10%, and 20% volume loads. Commercial sFRC with ARs of 20 and 100 were also tested. A tensilometer set up was used with moderate compliance, 5.4 J/cm<sup>2</sup> irradiance, and a C-factor of 2.75. Data was statistically analyzed using ANOVA followed by post hoc Tukey's test. The addition of 5% of the experimental fiber did not significantly increase stress while the 10% and 20% groups resulted in 36.3% and 39.1% higher stress values, respectively, compared to the non-fiber control group (p < 0.05). Of all the sFRC groups, the very low AR material exhibited the lowest stress [0.682 MPa (p = 0.001)] while another commercial material with higher AR fibers exhibited the highest overall value [1.822 MPa (p < 0.001)] when compared to the control group. The results indicate that both short fiber volume and AR are important variables to consider with regards to setting stresses of sFRC. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1930-1937, 2017.