Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Canadian mosquito species through DNA barcodes

Abstract A short fragment of mt DNA from the cytochrome c oxidase 1 (CO1) region was used to provide the first CO1 barcodes for 37 species of Canadian mosquitoes (Diptera: Culicidae) from the provinces Ontario and New Brunswick. Sequence variation was analysed in a 617‐bp fragment from the 5′ end of the CO1 region. Sequences of each mosquito species formed barcode clusters with tight cohesion that were usually clearly distinct from those of allied species. CO1 sequence divergences were, on average, nearly 20 times higher for congeneric species than for members of a species; divergences between congeneric species averaged 10.4% (range 0.2–17.2%), whereas those for conspecific individuals averaged 0.5% (range 0.0–3.9%).
Clinical experience with adult polycystic liver disease

Adult polycystic liver disease is characterized by multiple difluse cystic lesions of the liver, usually in association with polycystic kidney disease. Rarely, significant liver disease will produce enough symptoms to call for surgical attention. Symptoms range from simple compression to fatal liver failure. Treatment of seven patients (six women) with symptomatic polycystic liver disease over 18 months is reported. Rapidly progressing liver failure and sepsis from infected ascites following puncture developed in one patient and precluded surgery. Another presented with an acute abdomen and anaemia from liver cyst bleeding and was treated conservatively. Five patients with massive hepatomegaly and compression symptoms underwent fenestration and resection to debulk the cystic liver mass. No intra‐abdominal drains were used after operation and there were no hospital deaths. One patient developed a bile leak which was managed by percutaneous drainage. Clinical approach, complications and treatment options in adult polycystic liver disease are reviewed.
Hyperkyphotic Posture and Risk of Future Osteoporotic Fractures: The Rancho Bernardo Study

It is unknown whether kyphosis of the thoracic spine is an independent risk factor for future osteoporotic fractures. In 596 community‐dwelling women, we found that with increasing kyphosis, there was a significant trend of increasing fracture risk that was independent of previous history of fractures or BMD.
The Numerical Results of Diverse Systems of Breeding, with Respect to Two Pairs of Characters, Linked or Independent, with Special Relation to the Effects of Linkage.

Page 99, fifth line of footnote, for "Sewell Wright", read "Sewall Wright". Page 99, last line of footnote, for "B n F n -1 G n -1" read "B n -F n -1-G n -1". Page 117, interchange lines 18 and 19, placing "in sections (12), (13) and (14)" above the preceding line. Page 144, fourth line from
LASIK Induces Minimal Regrowth and No Haze Development in Rabbit Corneas

Purpose: To quantify central corneal regrowth and haze development after LASIK in rabbits. Methods: New Zealand White rabbits received an 89 μ m (–8 diopters) myopic LASIK and were evaluated during 4 months using slit-lamp and in vivo confocal microscopy to monitor changes in central corneal morphology, epithelial and stromal thickness, flap and bed thickness, and corneal light backscattering (haze). At various timepoints, corneas were processed for histology. Results: Using in vivo confocal microscopy, LASIK induced no detectable morphological changes besides a slightly elevated light backscattering at the interface. Correspondingly, all corneas remained clear with no haze development by slit-lamp biomicroscopy. Corneal thickness was stable by 8 weeks after an increase of 17 ± 4 μ m that consisted of a 13 ± 3 μ m stromal regrowth and a 4 ± 2 μ m epithelial hyperplasia. At the LASIK interface, less than 4 μ m new extracellular matrix was deposited. Accordingly, all LASIK flaps were easily pulled off by 6 months. Conclusions: LASIK induces a minimal wound healing response in rabbit corneas with no haze development and a regrowth (regression) of only 17 μ m of an 89-μ m photoablation. Three main factors contributed to the observed regrowth: epithelial hyperplasia (∼ 4 μ m), matrix deposition at the LASIK interface (∼ 4 μ m), and stromal growth outside the interface within the flap and wound bed (∼ 9 μ m).
Structure-based mutagenesis of the catalytic domain of human immunodeficiency virus type 1 integrase

Two different crystal structures of the human immunodeficiency virus type 1 (HIV-1) integrase (IN) catalytic domain were analyzed for interactions at the enzyme active site. Gln-62 and Glu-92 interact with active-site residue Asp-64, and Lys-136 interacts with active-site residue Asp-116 across a dimer interface. Conservative and nonconservative substitutions were introduced at these positions to probe the roles of these interactions in HIV-1 integration. Purified mutant proteins were assayed for in vitro 3' processing, DNA strand transfer, and disintegration activities, and HIV-1 mutants were assayed for virion protein composition, reverse transcription, and infectivities in human cell lines. Each of the mutant IN proteins displayed wild-type disintegration activity, indicating that none of the interactions is essential for catalysis. Mutants carrying Gln or Ala for Glu-92 displayed wild-type activities, but substituting Lys for Glu-92 reduced in vitro 3' processing and DNA strand transfer activities 5- to 10-fold and yielded a replication-defective IN active-site mutant viral phenotype. Substituting Glu for Gln-62 reduced in vitro 3' processing and DNA strand transfer activities 5- to 10-fold without grossly affecting viral replication kinetics, suggesting that HIV-1 can replicate in T-cell lines with less than the wild-type level of IN activity. The relationship between IN solubility and HIV-1 replication was also investigated. We previously showed that substituting Lys for Phe-185 dramatically increased the solubility of recombinant IN but caused an HIV-1 particle assembly defect. Mutants carrying His at this position displayed increased solubility and wild-type replication kinetics, showing that increased IN solubility per se is not detrimental to virus growth.
Sorafenib for patients with pretreated recurrent or progressive high-grade glioma: a retrospective, single-institution study

Therapeutic options for patients with pretreated advanced high-grade glioma (HGG) are limited. Sorafenib, a small molecule with multiple potential beneficial actions, appears particularly promising. We reviewed the outcomes of 30 patients with recurrent or progressive HGG treated with sorafenib within a named patient program. Overall, 16 patients suffered from recurrent or progressive glioblastoma multiforme and 14 patients had grade 3 gliomas. All but four patients had previously undergone surgical debulking; all but one patient had received previous standard multimodal treatment; and 18 patients (60%) had received more than one line of chemotherapy, in median three. Progression-free survival (PFS), defined as the time from initiation of sorafenib to treatment discontinuation because of tumor progression or death, was selected as the endpoint. The use of sorafenib resulted in a median PFS of 3 months [95% confidence interval (CI) 1.9–4.1 months] in patients with glioblastoma and of 3.1 months (95% CI 1.4–4.8 months) in patients with other HGG. The PFS-6 for the whole cohort was 23%. Sixteen patients reported adverse events, mostly moderate, with hypertension as the most frequently reported toxicity (seven patients). One patient died of cerebral bleeding (grade 5 toxicity). The overall survival after initiation of sorafenib was 6 months (95% CI 3.9–8.0 months) for patients with glioblastoma multiforme and 10 months (95% CI 3.1–16.9 months) for patients with HGG. In this retrospective analysis of heavily pretreated patients with HGG, sorafenib monotherapy was associated with tumor stabilization in a small subset of patients. The risk–benefit ratio was acceptable in the context of an apparent clinical benefit in patients with a fatal disease.
Stock Market Mispricing: Money Illusion or Resale Option?

Abstract We examine two hypotheses to explain stock mispricing: i) the money illusion hypothesis (Modigliani and Cohn (1979)) and ii) the resale option hypothesis (Scheinkman and Xiong (2003)). We find that the money illusion hypothesis may explain the level, but not the volatility, of mispricing in the U.S. market. In contrast, the stock resale option hypothesis, which stems from heterogeneous beliefs about future dividend growth rates and short-sale constraints, can explain both the level and the volatility of mispricing. The evidence suggests that while the two hypotheses complement each other in explaining the level of mispricing, the resale option hypothesis provides a more coherent explanation for asset price bubbles, in which extraordinarily high price levels are often accompanied by excessive volatility and frenzied trading.
The location of chitin in the yeast cell wall.

When chlorophyll a was left on silica gel G under an atmosphere of nitrogen, conversion into the 'changed' chlorophylls was greatly diminished. This suggests that these compounds are oxidized chlorophylls. The chlorophyll C-10 hydrogen may be replaced in 'changed' chlorophylls a-i and b-i by a hydroxyl group (not a methoxyl as in certain chlorophyll 'allomers'), and 'changed' chlorophylls a-2 and b-2 may be the optical isomers at C-10 of 'changed' chlorophylls a-i and b-1 respectively (Bacon & Holden, 1966). 'Changed' chlorophyll a-3, which is perhaps a mixture of isomers, may in addition have oxygen between C-9 and C10 in view ofits similarity topigmentsdescribedbyHolt (1958). The structure of 'changed' chlorophyll b-3 is probably analogousto thatof 'changed' chlorophylla-3. There have been many recent reports ofthe use of silica gel or kieselguhr for the chromatography of chloroplast pigments. The identities and purity of pigments separated on such adsorbents and assumed to be chlorophylls a and b should be checked by a sensitive chromatographic method causing little or no damage to the pigments. Rapid working with thin-layer chromatography on cellulose is suitable for this. The formation of altered chlorophylls may lead not only to errors of interpretation, particularly when these pigments are made more obvious by chromatography with a second solvent, but also to errors in quantitative analysis due, for example, to differences in molar extinction coefficients. Bleaching of the chlorophylls may also occur and affect recoveries. Carotenoids as well as chlorophylls can be damaged on some inorganic adsorbents (Strain, Sherma, Benton & Katz, 1965).
Terminal duct lobular unit involution of the normal breast: implications for breast cancer etiology.

BACKGROUND Greater degrees of terminal duct lobular unit (TDLU) involution have been linked to lower breast cancer risk; however, factors that influence this process are poorly characterized. METHODS To study this question, we developed three reproducible measures that are inversely associated with TDLU involution: TDLU counts, median TDLU span, and median acini counts/TDLU. We determined factors associated with TDLU involution using normal breast tissues from 1938 participants (1369 premenopausal and 569 postmenopausal) ages 18 to 75 years in the Susan G. Komen Tissue Bank at the Indiana University Simon Cancer Center. Multivariable zero-inflated Poisson models were used to estimate relative risks (RRs) and 95% confidence intervals (95% CIs) for factors associated with TDLU counts, and multivariable ordinal logistic regression models were used to estimate odds ratios (ORs) and 95% CIs for factors associated with categories of median TDLU span and acini counts/TDLU. RESULTS All TDLU measures started declining in the third age decade (all measures, two-sided P trend ≤ .001); and all metrics were statistically significantly lower among postmenopausal women. Nulliparous women demonstrated lower TDLU counts compared with uniparous women (among premenopausal women, RR = 0.79, 95% CI = 0.73 to 0.85; among postmenopausal, RR = 0.67, 95% CI = 0.56 to 0.79); however, rates of age-related TDLU decline were faster among parous women. Other factors were related to specific measures of TDLU involution. CONCLUSION Morphometric analysis of TDLU involution warrants further evaluation to understand the pathogenesis of breast cancer and assessing its role as a progression marker for women with benign biopsies or as an intermediate endpoint in prevention studies.
Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+ Ions and the Hydrogen-Bonding Network in the Active Site

The recently discovered twister ribozyme is thought to utilize general acid–base catalysis in its self-cleavage mechanism, but the roles of nucleobases and metal ions in the mechanism are unclear. Herein, molecular dynamics simulations of the env22 twister ribozyme are performed to elucidate the structural and equilibrium dynamical properties, as well as to examine the role of Mg2+ ions and possible candidates for the general base and acid in the self-cleavage mechanism. The active site region and the ends of the pseudoknots were found to be less mobile than other regions of the ribozyme, most likely providing structural stability and possibly facilitating catalysis. A purported catalytic Mg2+ ion and the closest neighboring Mg2+ ion remained chelated and relatively immobile throughout the microsecond trajectories, although removal of these Mg2+ ions did not lead to any significant changes in the structure or equilibrium motions of the ribozyme on the microsecond time scale. In addition, a third metal ion, a Na+ ion remained close to A1(O5′), the leaving group atom, during the majority of the microsecond trajectories, suggesting that it might stabilize the negative charge on A1(O5′) during self-cleavage. The locations of these cations and their interactions with key nucleotides in the active site suggest that they may be catalytically relevant. The P1 stem is partially melted at its top and bottom in the crystal structure and further unwinds in the trajectories. The simulations also revealed an interconnected network comprised of hydrogen-bonding and π-stacking interactions that create a relatively rigid network around the self-cleavage site. The nucleotides involved in this network are among the highly conserved nucleotides in twister ribozymes, suggesting that this interaction network may be important to structure and function.
Cognitive contributions to gait and falls: Evidence and implications

Dementia and gait impairments often coexist in older adults and patients with neurodegenerative disease. Both conditions represent independent risk factors for falls. The relationship between cognitive function and gait has recently received increasing attention. Gait is no longer considered merely automated motor activity but rather an activity that requires executive function and attention as well as judgment of external and internal cues. In this review, we intend to: (1) summarize and synthesize the experimental, neuropsychological, and neuroimaging evidence that supports the role played by cognition in the control of gait; and (2) briefly discuss the implications deriving from the interplay between cognition and gait.
Long-Term Functional Outcome after Unilateral Cordectomy

Purpose of the Study: Our aim was to longitudinally analyze the vocal outcome after endoscopic CO2 laser resection of early glottic carcinoma. Procedures: Sixteen patients treated with laser surgery for T1 or T2 tumors of the vocal cords received voice therapy and were examined 1, 2, 3, 4.5, 6 and 12 months postoperatively. Besides videolaryngostroboscopy, each examination included history, phonetogram of the speaking and the singing voice, language-specific hoarseness diagram and a questionnaire (Voice Handicap Index 12 in German). Results: Objective parameters demonstrated a broad variability with a slight tendency of improvement over time. For the maximal phonation time a nearly constant improvement was seen. After an initial improvement deterioration for subjective assessment in the Voice Handicap Index was noted in most patients 3–6 months postoperatively. Conclusions: The functional outcome after cordectomy is variable. Message of the Paper: Discrepancies between objective findings and patient satisfaction over time have to be considered after cordectomy.
The faroes statement: human health effects of developmental exposure to chemicals in our environment.

The periods of embryonic, foetal and infant developmentare remarkably susceptible to environmental hazards. Toxicexposures to chemical pollutants during these windows ofincreased susceptibility can cause disease and disability ininfants, children and across the entire span of human life.Among the effects of toxic exposures recognized in the pasthave been spontaneous abortion, congenital malformations,lowered birthweight and other adverse effects. These outcomesmay be readily apparent. However, even subtle changes causedby chemical exposures during early development may leadto important functional deficits and increased risks ofdisease later in life. The timing of exposure during early lifehas therefore become a crucial factor to be considered intoxicological assessments.During 20–24 May 2007, researchers in the fields of environmentalhealth, environmental chemistry, developmentalbiology, toxicology, epidemiology, nutrition and paediatricsgathered at the International Conference on Fetal Programmingand Developmental Toxicity, in Torshavn, FaroeIslands. The conference goal was to highlight new insightsinto the effects of prenatal and early postnatal exposure tochemical agents, and their sustained effects on the individualthroughout the lifespan. The conference brought togetherresearchers to focus on human data and the translationof laboratory results to elucidate the environmental risks tohuman health.
Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias

A Rickettsia bacterium promotes its own geographical spread by manipulating its insect host’s sex ratio and fecundity. Maternally inherited bacterial symbionts of arthropods are common, yet symbiont invasions of host populations have rarely been observed. Here, we show that Rickettsia sp. nr. bellii swept into a population of an invasive agricultural pest, the sweet potato whitefly, Bemisia tabaci, in just 6 years. Compared with uninfected whiteflies, Rickettsia-infected whiteflies produced more offspring, had higher survival to adulthood, developed faster, and produced a higher proportion of daughters. The symbiont thus functions as both mutualist and reproductive manipulator. The observed increased performance and sex-ratio bias of infected whiteflies are sufficient to explain the spread of Rickettsia across the southwestern United States. Symbiont invasions such as this represent a sudden evolutionary shift for the host, with potentially large impacts on its ecology and invasiveness.
Comparative Diagenesis and Rare Earth Element Variation in Miocene Invertebrate and Vertebrate Fossils from Panama

The incorporation of rare earth elements (REEs) into the mineral lattices of skeletonized fossils has been used, particularly in vertebrates, to understand diagenesis and other postmortem paleoenvironmental parameters. Little is known about similar processes in invertebrates. Invertebrate and vertebrate fossils were analyzed for REE concentrations and patterns from five Miocene formations in central Panama (∼20–6 m.yr. ago). These formations (Culebra, Cucaracha, Gatun, Chucunaque, and Chagres) contain sediments interpreted to range from freshwater to shallow marine environments (depth of <300 m). We also compared different compositional types of fossils, including hydroxylapatite (bone) and aragonite (otoliths) in vertebrates and calcite and aragonite in invertebrates. REEs from modern invertebrates indicate that, as previously reported for vertebrates, invertebrates do not incorporate significant amounts of REEs into their mineral lattices during life; therefore, uptake must primarily occur during diagenesis. Comparisons of REEN concentrations (REE concentrations normalized to Post-Archean Australian Shale) of the fossils from Panama indicate differences in diagenesis. Within our largest sample from the Gatun Formation, there are significance differences in REEN concentrations and patterns within different compositional types. For example, shark teeth have the highest REEN concentrations and otoliths the lowest, with these differences likely a result of physical, chemical, and mineralogical factors. Calcitic and aragonitic fossils from the Gatun Formation show REEN patterns indicating differential uptake of individual elements during diagenesis. The cerium anomaly, previously used to indicate relative paleobathymetry, did not discriminate water depth in the marine formations. Comparative analysis of REEs in vertebrates and invertebrates provides a powerful tool to understand diagenetic processes, as demonstrated in the five formations and different compositional types studied from the Miocene of Panama.
Fatigue Behavior of Computer-Aided Design/Computer-Assisted Manufacture Ceramic Abutments as a Function of Design and Ceramics Processing.

PURPOSE Zirconia is being widely used, at times apparently by simply copying a metal design into ceramic. Structurally, ceramics are sensitive to both design and processing (fabrication) details. The aim of this work was to examine four computer-aided design/computer-assisted manufacture (CAD/CAM) abutments using a modified International Standards Organization (ISO) implant fatigue protocol to determine performance as a function of design and processing. MATERIALS AND METHODS Two full zirconia and two hybrid (Ti-based) abutments (n = 12 each) were tested wet at 15 Hz at a variety of loads to failure. Failure probability distributions were examined at each load, and when found to be the same, data from all loads were combined for lifetime analysis from accelerated to clinical conditions. RESULTS Two distinctly different failure modes were found for both full zirconia and Ti-based abutments. One of these for zirconia has been reported clinically in the literature, and one for the Ti-based abutments has been reported anecdotally. The ISO protocol modification in this study forced failures in the abutments; no implant bodies failed. Extrapolated cycles for 10% failure at 70 N were: full zirconia, Atlantis 2 × 10(7) and Straumann 3 × 10(7); and Ti-based, Glidewell 1 × 10(6) and Nobel 1 × 10(21). Under accelerated conditions (200 N), performance differed significantly: Straumann clearly outperformed Astra (t test, P = .013), and the Glidewell Ti-base abutment also outperformed Atlantis zirconia at 200 N (Nobel ran-out; t test, P = .035). CONCLUSION The modified ISO protocol in this study produced failures that were seen clinically. The manufacture matters; differences in design and fabrication that influence performance cannot be discerned clinically.