Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution and diversity of copy number variation in the great ape lineage

Copy number variation (CNV) contributes to disease and has restructured the genomes of great apes. The diversity and rate of this process, however, have not been extensively explored among great ape lineages. We analyzed 97 deeply sequenced great ape and human genomes and estimate 16% (469 Mb) of the hominid genome has been affected by recent CNV. We identify a comprehensive set of fixed gene deletions (n = 340) and duplications (n = 405) as well as >13.5 Mb of sequence that has been specifically lost on the human lineage. We compared the diversity and rates of copy number and single nucleotide variation across the hominid phylogeny. We find that CNV diversity partially correlates with single nucleotide diversity (r2 = 0.5) and recapitulates the phylogeny of apes with few exceptions. Duplications significantly outpace deletions (2.8-fold). The load of segregating duplications remains significantly higher in bonobos, Western chimpanzees, and Sumatran orangutans—populations that have experienced recent genetic bottlenecks (P = 0.0014, 0.02, and 0.0088, respectively). The rate of fixed deletion has been more clocklike with the exception of the chimpanzee lineage, where we observe a twofold increase in the chimpanzee–bonobo ancestor (P = 4.79 × 10−9) and increased deletion load among Western chimpanzees (P = 0.002). The latter includes the first genomic disorder in a chimpanzee with features resembling Smith-Magenis syndrome mediated by a chimpanzee-specific increase in segmental duplication complexity. We hypothesize that demographic effects, such as bottlenecks, have contributed to larger and more gene-rich segments being deleted in the chimpanzee lineage and that this effect, more generally, may account for episodic bursts in CNV during hominid evolution.
Effect of monensin sodium on lactational performance of autumn- and spring-calving cows

Monensin sodium is widely used to manipulate ruminal fermentation (Bergen & Bates, 1984), with the aim of increasing energy supply to the animal. Monensin has been most widely used in diets of beef cattle and young growing dairy cattle, particularly in confinement management systems, where the ionophore can be mixed directly into the ration. Accurate daily dosing of grazing ruminants with small quantities of rumen modifiers, such as ionophores, proved particularly labour-intensive and expensive until the development of the controlled-release capsule (CRC; Laby et al. 1984). Subsequently a commercially available CRC containing monensin sodium was developed (Elanco Animal Health, Cambridge, NZ) facilitating its use in grazing animals. It has also been tested as a method of reducing the incidence of bloat in lactating dairy cows grazing pastures containing legumes.
Stearoyl-CoA Desaturase 2 Is Required for Peroxisome Proliferator-activated Receptor γ Expression and Adipogenesis in Cultured 3T3-L1 Cells*

Based on recent evidence that fatty acid synthase and endogenously produced fatty acid derivatives are required for adipogenesis in 3T3-L1 adipocytes, we conducted a small interfering RNA-based screen to identify other fatty acid-metabolizing enzymes that may mediate this effect. Of 24 enzymes screened, stearoyl-CoA desaturase 2 (SCD2) was found to be uniquely and absolutely required for adipogenesis. Remarkably, SCD2 also controls the maintenance of adipocyte-specific gene expression in fully differentiated 3T3-L1 adipocytes, including the expression of SCD1. Despite the high sequence similarity between SCD2 and SCD1, silencing of SCD1 did not down-regulate 3T3-L1 cell differentiation or gene expression. SCD2 mRNA expression was also uniquely elevated 44-fold in adipose tissue upon feeding mice a high fat diet, whereas SCD1 showed little response. The inhibition of adipogenesis caused by SCD2 depletion was associated with a decrease in peroxisome proliferator-activated receptor γ (PPARγ) mRNA and protein, whereas in mature adipocytes loss of SCD2 diminished PPARγ protein levels, with little change in mRNA levels. In the latter case, SCD2 depletion did not change the degradation rate of PPARγ protein but decreased the metabolic labeling of PPARγ protein using [35S]methionine/cysteine, indicating protein translation was decreased. This requirement of SCD2 for optimal protein synthesis in fully differentiated adipocytes was verified by polysome profile analysis, where a shift in the mRNA to monosomes was apparent in response to SCD2 silencing. These results reveal that SCD2 is required for the induction and maintenance of PPARγ protein levels and adipogenesis in 3T3-L1 cells.
High-frequency oscillation in the rescue of infants with persistent pulmonary hypertension.

High-frequency oscillatory ventilation (HFOV) was used to treat 41 infants with persistent pulmonary hypertension of the newborn (PPHN). Of the 37 patients who showed early improvement on HFOV, three died. The remaining 34 patients demonstrated, within one hour of the switchover to HFOV, a rise in mean arterial/alveolar oxygen tension ratio (PaO2/PaO2) from 0.093 +/- 0.041 (SD) to 0.132 +/- 0.051 (p less than .001), and a fall in mean PaCO2 from 42 +/- 10 to 34 +/- torr 9 (p less than .01). Mean airway pressure (Paw) fell significantly (p less than .01) within 12 h. The mean duration of conventional mechanical ventilation before starting HFOV was longer in 13 patients who developed bronchopulmonary dysplasia (BPD) than in 21 non-BPD patients (44.7 +/- 32.3 vs. 19.1 +/- 15.6 h, p less than .002), as was the duration of exposure to Paw greater than 15 cm H2O during that treatment mode (31.8 +/- 21.3 vs. 9.5 +/- 6.0 h, p less than .001). HFOV is often effective in the treatment of patients with PPHN, and early initiation of this type of mechanical ventilation may be associated with a reduced incidence of BPD.
Transport AC Loss Measurements of a Triangular Epoxy-Impregnated High-Temperature Superconducting Coil

In this paper, the transport ac losses in a triangular epoxy-impregnated high-temperature superconducting (HTS) coil made from YBCO coated conductor, intended for use in a prototype axial flux HTS electric machine, are measured using two different electrical techniques at 77 K. The first set of ac loss measurements of the coil are carried out at the University of Cambridge using a technique based on a lock-in amplifier. The coil is then measured at the Center for Advanced Power Systems, Florida State University, using a technique based on a high-accuracy data acquisition measurement system. The two different methods show consistent results, validating the accuracy of these two techniques for transport ac loss measurements of superconducting coils. Multiple voltage taps are utilized within the coil to study the details and distribution of the ac loss in different sections of the coil. Losses are also measured with a flux diverter made of ferromagnetic material to analyze its effect on the ac losses.
Propagated Endothelial Ca2+ Waves and Arteriolar Dilation In Vivo: Measurements in Cx40BAC-GCaMP2 Transgenic Mice

To study endothelial cell (EC)- specific Ca2+ signaling in vivo we engineered transgenic mice in which the Ca2+ sensor GCaMP2 is placed under control of endogenous connexin40 (Cx40) transcription regulatory elements within a bacterial artificial chromosome (BAC), resulting in high sensor expression in arterial ECs, atrial myocytes, and cardiac Purkinje fibers. High signal/noise Ca2+ signals were obtained in Cx40BAC-GCaMP2 mice within the ventricular Purkinje cell network in vitro and in ECs of cremaster muscle arterioles in vivo. Microiontophoresis of acetylcholine (ACh) onto arterioles triggered a transient increase in EC Ca2+ fluorescence that propagated along the arteriole with an initial velocity of ≈116 &mgr;m/s (n=28) and decayed over distances up to 974 &mgr;m. The local rise in EC Ca2+ was followed (delay, 830±60 ms; n=8) by vasodilation that conducted rapidly (mm/s), bidirectionally, and into branches for distances exceeding 1 mm. At intermediate distances (300 to 600 &mgr;m), rapidly-conducted vasodilation occurred without changing EC Ca2+, and additional dilation occurred after arrival of a Ca2+ wave. In contrast, focal delivery of sodium nitroprusside evoked similar local dilations without Ca2+ signaling or conduction. We conclude that in vivo responses to ACh in arterioles consists of 2 phases: (1) a rapidly-conducted vasodilation initiated by a local rise in EC Ca2+ but independent of EC Ca2+ signaling at remote sites; and (2) a slower complementary dilation associated with a Ca2+ wave that propagates along the endothelium.
A Miniature Fiber-Optic Refractive-Index Sensor Based on Laser-Machined Fabry–Perot Interferometer Tip

A novel miniature fiber-optic Fabry-Perot (F-P) refractive-index (RI) sensor machined by 157 nm laser is proposed. The sensor head consists of a micro air F-P cavity near the tip of a single-mode fiber with a micro channel on the fiber tip used as both inlet and outlet for medium under test. Thin films are coated at reflective interfaces of the F-P cavity as mirrors to ensure high optical contrast, respectively. A RI resolution of 1130.887 nm/RI unit (RIU) is achieved by experiment. Such a sensor has a number of outstanding advantages when compared with other fiber-optic RI sensors, such as very small, rigid, high resolution, excellent linearity, wide measurement range, et al.
Deaths of children in Greater London 1966.

Senior Medical Statisticiant, General Register Office Thehighdeath rate amonginfants atorimmediately after birth compared withthatforolder children hasfocused attention ontheprevention of perinatal andinfant mortality andcomparatively little notice hasbeentaken ofwhathasbeenhappening tothemortality rates amongolder children inthelast 10years orso. The1940s werecharacterized byarapid decline inmortality rates ofallchildren inEngland and Wales. Thespeed ofdecline ofinfant mortality rates slowed during thelate 1940s andearly 1950s but, except forashort pause atthebeginning ofthe 1960s, hascontinued todecrease steadily until the present time(Fig. 1). Theolder children showa different pattern. Therapid dropinthe1940s, generally attributed toantibiotics andimmunization, continued witha decreased momentumuntil the
Barrier Activity in Candida albicans Mediates Pheromone Degradation and Promotes Mating

ABSTRACT Mating in Candida albicans and Saccharomyces cerevisiae is regulated by the secretion of peptide pheromones that initiate the mating process. An important regulator of pheromone activity in S. cerevisiae is barrier activity, involving an extracellular aspartyl protease encoded by the BAR1 gene that degrades the alpha pheromone. We have characterized an equivalent barrier activity in C. albicans and demonstrate that the loss of C. albicans BAR1 activity results in opaque a cells exhibiting hypersensitivity to alpha pheromone. Hypersensitivity to pheromone is clearly seen in halo assays; in response to alpha pheromone, a lawn of C. albicans Δbar1 mutant cells produces a marked zone in which cell growth is inhibited, whereas wild-type strains fail to show halo formation. C. albicans mutants lacking BAR1 also exhibit a striking mating defect in a cells, but not in α cells, due to overstimulation of the response to alpha pheromone. The block to mating occurs prior to cell fusion, as very few mating zygotes were observed in mixes of Δbar1a and α cells. Finally, in a barrier assay using a highly pheromone-sensitive strain, we were able to demonstrate that barrier activity in C. albicans is dependent on Bar1p. These studies reveal that a barrier activity to alpha pheromone exists in C. albicans and that the activity is analogous to that caused by Bar1p in S. cerevisiae.
Comparison of Vitex agnus castus Extract and Pergolide in Treatment of Equine Cushing ’ s Syndrome

Pituitary pars intermedia hyperplasia, which causes Equine Cushing’s Syndrome, has been treated with dopaminergic agonists such as pergolide. Vitex agnus castus (Chaste Berry) extract has been used medicinally for centuries for various human female cycle disorders, and a lay article claimed its therapeutic efficacy in horses with pituitary hyperplasia and other hormonal dysfunction. Ethanol extracts of the seeds have been demonstrated to bind to the D2 receptor of rat pituitary cells and inhibit prolactin secretion. To our knowledge it is unknown whether Vitex agnus castus extract affects secretion of plasma ACTH or pro-opiomelanocortin (POMC)s. Pergolide is a dopaminergic agonist at D2 receptor sites in vitro, although there are no specific studies in horses. Elevated concentrations of POMCs and plasma ACTH have been measured in horses with pituitary hyperplasia. Pergolide has been shown to affect plasma POMC and plasma ACTH concentrations in horses. Because of increasing interest in the use of Vitex agnus castus in horses, we conducted a study on the effects of a commercially available product marketed for use in horses (Vitex agnus castus Extract) and compared it with the effect of pergolide.
Handbook of Culture of Abalone and Other Marine Gastropods

Antibodies Matthew R. Kaser and Gary C. Howard Antigens Paul Algate, Jory Baldridge, and Sally Mossman Adjuvants Jory Baldridge, Paul Algate, and Sally Mossman Production of Polyclonal Antibodies Lon V. Kendall Production of Monoclonal Antibodies Kathleen C. F. Sheehan Quantitative Production of Monoclonal Antibodies David A. Fox and Elizabeth M. Smith Purification and Characterization of Antibodies Joseph P. Chandler Making Antibodies in Bacteria Frederic A. Fellouse and Sachdev S. Sidhu Chemical and Proteolytic Modification of Antibodies George P. Smith Applications Lee Bendickson and Marit Nilsen-Hamilton Immunohistochemical Methods Jose A. Ramos-Vara and Julie Ackerman Saettele Immunoelectron Microscopy Sara E. Miller and David N. Howell Flow Cytometry Kristi R. Harkins and M. Elaine Kunze ELISAs John Chen and Gary C. Howard Antibodies in the Future: Challenges and Opportunities Matthew R. Kaser and Gary C. Howard
Is the ideal mother a sensitive mother? Beliefs about early childhood parenting in mothers across the globe

In this article, we test the hypothesis that beliefs about the ideal mother are convergent across cultures and that these beliefs overlap considerably with attachment theory’s notion of the sensitive mother. In a sample including 26 cultural groups from 15 countries around the globe, 751 mothers sorted the Maternal Behavior Q-Set to reflect their ideas about the ideal mother. The results show strong convergence between maternal beliefs about the ideal mother and attachment theory’s description of the sensitive mother across groups. Cultural group membership significantly predicted variations in maternal sensitivity belief scores, but this effect was substantially accounted for by group variations in socio-demographic factors. Mothers living in rural versus urban areas, with a low family income, and with more children, were less likely to describe the ideal mother as highly sensitive. Cultural group membership did remain a significant predictor of variations in maternal sensitivity belief scores above and beyond socio-demographic predictors. The findings are discussed in terms of the universal and culture-specific aspects of the sensitivity construct.
Supercritical fluids for high-power switching

Fast and repetitive switching in high-power circuits is a challenging task where the ultimate solutions still have to be found. Areas of application are pulsed power technology and power stations. We proposed a new approach. Supercritical fluids have insulation strength and thermal properties like liquids and fluidity, self-healing and absence of bubbles like gases. That's why we start investigating the subject of plasma switches in supercritical media. First results indicate excellent switch recovery and high insulation strength.
Natural Selection for Miillerian Mimicry in Heliconius erato in Costa Rica

The natural color pattern of individuals of the unpalatable and mimetic butterfly Heliconius erato was altered to a unique nonmimetic pattern. When returned to natural populations, the nonmimetic individuals remained for shorter periods of time and received more wing damage indicative of predator attacks than did the controls. The results indicate that M�llerian mimicry was functioning to protect the butterflies from predation.
The Adult Memory and Information Processing Battery (AMIPB) test of information-processing speed: a study of its reliability and feasibility in patients with multiple sclerosis

Objective: To investigate how useful the Adult Memory and Information Processing Battery Task A (AMIPB) is as a test of the speed of information processing in patients with multiple sclerosis (MS) by comparing various methods of presenting the test and assessing the reliability (test–retest and inter-rater) and utility of each version. Design: Each patient was assessed twice verbally by the same assessor 1–2 weeks apart. Then 1–2 weeks later half were assessed by another observer, and half were assessed by the first observer using a written method. Setting: A specialist young disabled unit. Subjects: Thirty-three patients with MS. Measures: The AMIPB, the Short Memory-Orientation-Concentration Test (SOMC) and the Barthel ADL Index. Results: The average (SD) number of correct responses after 4 min was 23.3 (18.6), median 21. The test–retest reliability (n = 24) of the 4-min AMIPB was high (r = 0.98) and the difference of the score ranged from –7 to 9: median 3, mean (SD) 1.88 (4.01) and interquartile range 0 to 3.25. The inter-observer reliability (n = 12) of the 4-min AMIPB was also high (r = 0.97) and the mean (SD) differences between scores were 4.3 (5.8), median 4, range +19 to –2. The score at 60 seconds and the score at 240 seconds were highly correlated (r = 0.98). The scores obtained verbally and by writing were closely correlated (r = 0.99). Conclusions: The AMIPB used over 120 seconds with verbal responses is a reliable and reasonable test for major information-processing deficits.
Ogon/Secreted Frizzled functions as a negative feedback regulator of Bmp signaling

The zebrafish mutant ogon (also called mercedes and short tail) displays ventralized phenotypes similar to the chordino (dino) mutant, in which the gene for the Bmp antagonist Chordin is mutated. We isolated the gene responsible for ogon by a positional cloning strategy and found that the ogon locus encodes a zebrafish homolog of Secreted Frizzled (Sizzled), which has sequence similarity to a Wnt receptor, Frizzled. Unlike other secreted Frizzled-related proteins (sFrps) and the Wnt inhibitor Dickkopf1, the misexpression of Ogon/Sizzled dorsalized, but did not anteriorize, the embryos, suggesting a role for Ogon/Sizzled in Bmp inhibition. Ogon/Sizzled did not inhibit a Wnt8-dependent transcription in the zebrafish embryo. ogon/sizzled was expressed on the ventral side from the late blastula through the gastrula stages. The ventral ogon/sizzled expression in the gastrula stage was reduced or absent in the swirl/bmp2b mutants but expanded in the chordino mutants. Misexpression of ogon/sizzled did not dorsalize the chordino mutants, suggesting that Ogon/Sizzled required Chordin protein for dorsalization and Bmp inhibition. These data indicate that Ogon/Sizzled functions as a negative regulator of Bmp signaling and reveal a novel role for a sFrp in dorsoventral patterning.
Determinants of the spatial distribution of tree species in a neotropical forest

De mechanismen die de ruimtelijke verspreidingdeling van soorten bepalen zijn verdeeld in twee uitersten: deterministisch (soortspecifieke aanpassing aan de omgevingsomstandigheden) en stochastisch (dispersielimitatie en stochastische demografie). Verschillende onderzoeken kijken naar deze twee mechanismen, maar de resultaten varieren sterk als gevolg van het ontbreken van een expliciete afweging van een kritiek component: ruimtelijke schaal. Eerdere studies die stochastische en deterministische processen in tropische bossen poogden te ontrafelen leverden vaak tegenstrijdige uitkomsten op. Dit leidt tot een mogelijke onderschatting van het belang van deterministische/stochastische processen. In dit proefschrift heb ik de verspreiding van zes soorten tropische bomen gekwantificeerd en heb ik het relatieve belang van omgevingsvariabelen (onderdeel van de deterministische processen) en beperking van in zaadproductie (onderdeel van de stochastische processen) geevalueerd. Ik heb ‘remote sensing’-technieken gecombineerd met veldexperimenten om zo beperkingen in zaadproductie en beperkingen in vestiging te kunnen koppelen, en. Daarbij heb ik in het beginstadium om het relatieve belang van stochastische en deterministische processen bij het bepalen van in het beginstadium de boomsoort recruitment in te geschatten. Het onderzoek leverde drie belangrijke bevindingen op: i) ruimtelijke schaal heeft een bepalend effect op leefomgeving associatieonderzoeken, ii) zaadpredatie hangt af van de dichtheid van conspecifieke en heterospecifieke plantsoorten dichtheid, iii) zaad- en vestigingbeperking bepalen de ruimtelijke verdeling in de vroege stadia van de recruitment. Deze bevindingen suggereren dat het relatieve belang van stochastische en deterministische processen die soortdistributie beinvloeden afhangt van de omvang van de studie en ecologische factoren die continu veranderen in tijd en in ruimte.
Toxicity of a 24-Hour Infusion of Gemcitabine in Biliary Tract and Pancreatic Cancer: A Pilot Study

The antitumor activity of gemcitabine is not dose-response related but schedule-dependent. Based on the results of a published phase I study in patients with non-small-cell lung cancer we started a pilot study of a 24-hr infusion of gemcitabine in patients with adenocarcinoma of the pancreas and biliary tract cancer. Twenty-five patients were enrolled and received a 24-hr infusion of gemcitabine once weekly on three consecutive out of 4 weeks. Dose levels of gemcitabine ranged from 100 to 150 mg/m2. One of 13 chemotherapy-naive patients had a partial response. Dose-limiting toxicity (DLT) was thrombocytopenia in pretreated patients and neutropenia in chemotherapy-naive patients. Other toxicities were oral mucositis, fever, flu-like symptoms, and asthenia. Maximum tolerated dose (MTD), especially in pretreated patients, was 100 mg/m2.
A Study of a GEM Tracking Detector for Imaging Positrons from PET Radioisotopes in Plants

Positron Emission Tomography is a powerful imaging technique used for humans and animals that can also be used to study plant biology. However, since many of the structures found on plants (e.g., leaves) are very thin, a large portion of the positrons emitted from PET isotopes escape before annihilation, leading to low efficiency and quantification inaccuracies. In this study, a gas tracking detector was used to measure escaping positrons from PET radiotracer isotopes which has the ability to reconstruct three dimensional tracks that can be used to form an image of the emitting object. This device uses a triple GEM detector with a short drift region and an XY strip readout plane to measure a vector for positrons passing through a drift gap. By projecting each particle track back to the object surface, a 2-D image of the spatial distribution of the positrons that escaped from that surface can be reconstructed. In this paper, we will describe the basic principle of the GEM detector and present results on its performance using various types of phantoms and actual plant specimens. Monte Carlo simulations are also used to better understand the detector performance and compare to actual measurements.