Miracle-dz/UniFAR-FTUs huggingface dataset:
Peripheral Refraction in Orthokeratology Patients

Purpose. The purpose of this study is to measure refraction across the horizontal central visual field in orthokeratology patients before and during treatment. Methods. Refractions were measured out to 34° eccentricity in both temporal and nasal visual fields using a free-space autorefractor (Shin-Nippon SRW5000) for the right eyes of four consecutively presenting myopic adult patients. Measurements were made before orthokeratology treatment and during the course of treatment (usually 1 week and 2 weeks into treatment). Refractions were converted into mean sphere (M), 90° to 180° astigmatism (J180), and 45° to 135° astigmatism (J45) components. Results. Before treatment, subjects had either a relatively constant mean sphere refraction across the field or a relative hypermetropia in the periphery as compared with the central refraction. As a result of treatment, myopia decreased but at reduced rate out into the periphery. Most patients had little change in mean sphere at 30° to 34°. In all patients, the refraction pattern altered little after the first week. Conclusion. Orthokeratology can correct myopia over the central ± 10° of the visual field but produces only minor changes at field angles larger than 30°. If converting relative peripheral hypermetropia to relative peripheral myopia is a good way of limiting the axial elongation that leads to myopia, orthokeratology is an excellent option for achieving this.
Characterization of Genetic Basis on Synergistic Interactions between Root Architecture and Biological Nitrogen Fixation in Soybean

Soybean [Glycine max (L.) Merr] is an important legume crop and its yield largely depends on root architecture (RA) and biological nitrogen fixation (BNF). However, the relationship between RA and BNF, and its genetics behind remain unclear. Here, two soybean genotypes contrasting in RA and their 175 F9:11 recombinant inbred lines (RILs) were evaluated in field. The shallow-root parent, JD12, had better nodulation and higher yield than the deep-root parent, NF58. Strong correlations between shoot dry weight (SDW) and RA or BNF traits existed in the RILs, and the shallow-root group had more and heavier nodules, as well as higher SDW. After inoculating with rhizobia, roots became shallower and bigger, showing strong synergistic interactions between RA and BNF. In total, 70 QTLs were identified for the 21 tested traits. Among them, qBNF-RA-C2, qBNF-RA-O, and qBNF-RA-B1, were newly identified QTLs for BNF and/or RA traits in soybean, which co-located with the QTLs for SDW detected presently, and with the QTLs for yield identified previously. The results together suggest that there are synergistic interactions between RA and BNF, and the QTLs identified here could be used for breeding new soybean varieties with higher yields through optimization of RA traits and BNF capacity.
Evaluation of race distance, track surface and season of the year on exercise-induced pulmonary haemorrhage in flat racing thoroughbreds in Brazil.

REASONS FOR PERFORMING STUDY To our knowledge no studies evaluating risk factors to EIPH have been undertaken with such a population of horses in Brazil, which is one of the few countries in the racing community to accept the use of frusemide (FUR) as a prerace medication for bleeders. We also compared national results with those already in the literature. OBJECTIVES To verify the influence of variables such as distance of the race, racetrack surface, going and season of the year in the recurrence and severity of EIPH and its effect on the finishing position of flat racing Thoroughbreds in Brazil. METHODS 2118 post race respiratory endoscopies were recorded, in a total of 1003 individual horses. All horses in the study were certified bleeders (deemed positive by registered veterinarians following one or more endoscopies) and were administered FUR prior to each race. Data was analysed using both ordinary logistic regression and multiple logistic regression. RESULTS The results suggest that race distance, season of the year and racetrack surface affect the recurrence of EIPH. Also, despite the use of FUR, the majority (62%) of horses continued to display some degree of haemorrhage. CONCLUSIONS There was a tendency for horses that remained positive despite the use of FUR to finish unplaced in a race. Horses which had a significant reduction in bleeding and became HPIE negative after the use of FUR, tended to finish in top positions. It was not possible to determine a pattern of severity of EIPH in horses with more than one endoscopy. Further studies are required to improve our understanding of this syndrome and its correlations to performance in the racing Thoroughbred, together with the role of FUR and its possible enhancing performance effects and efficacy in consistently diminishing EIPH. POTENTIAL RELEVANCE This study enabled a better understanding of the use of FUR in Brazilian Thoroughbred racehorses and showed there was a tendency towards improvement in performance after administrion of FUR in bleeders. The fact that a large number of horses remained positive for EIPH despite the use of FUR should encourage the scientific community to search for better ways of reducing, or preventing, this syndrome.
Direct real-time PCR examination for Mycobacterium tuberculosis in respiratory samples can be cost effective

Aim: To assess whether the use of direct realtime polymerase chain reaction (PCR) on smear-positive sputa can be cost-effective, by speciating mycobacteria earlier than current methods and thereby preventing unnecessary screening tests as part of the contact tracing process. Methods: A retrospective study of all patients with smear-positive sputa in a Liverpool teaching hospital between 2004 and 2007. All the PCRs performed on these patients were reviewed and compared them with their mycobacterial culture results. Unit costs for PCR, chest X-ray (CXR), tuberculin skin test (TST), interferon-gamma (IFN-γ) and medical/nursing time were conservatively estimated at £50, £11, £10, £40 and £30 respectively. The total PCR costs were compared with the costs of unnecessary follow up of patients, negative for Mycobacterium tuberculosis (MTB) by PCR, subsequently confirmed to be MTB culture negative. Results: 203 smear-positive patients underwent direct PCR testing. 126 (62%) patients grew Mycobacterium tuberculosis (MTB), 74 (37%) had environmental mycobacterial infection (EMI) and 3 (1%) were culture negative. Of the 126 patients’ culture positive MTB patients, 123 were PCR positive and 3 PCR negative. Of the 77 patients that were culture negative for MTB, 75 were PCR negative and 2 PCR positive The sensitivity, specificity, positive and negative predictive values for direct PCR versus MTB culture were 98%, 96%, 98% and 97% respectively. Total costs of all PCRs performed amounted to £10,150. The cost of contact procedures for PCR-negative and MTB culturenegative index cases was estimated at £19,650. This equated to a total saving of £9,500 in contact tracing costs. Conclusions: Direct PCR examination testing of smear-positive patients can be cost-effective in areas where there is a high incidence of EMI.
Visceral ischemia and organ dysfunction after thoracoabdominal aortic aneurysm repair. A clinical and cost analysis.

OBJECTIVE Repair of thoracoabdominal aortic aneurysms (TAAAs) is associated with significant postoperative morbidity and mortality. Reperfusion of acutely ischemic abdominal viscera in animals leads to release of multiple factors that cause local and distant organ damage, and similar phenomena occurring in humans after TAAA repair could contribute to the high morbidity/mortality and cost associated with this procedure. METHODS Twenty-nine patients undergoing elective TAAA repair were studied prospectively. Preoperative organ dysfunction and intraoperative risk factors (cross-clamp time, blood loss, operative time) were assessed and compared with postoperative organ dysfunction (defined as: pulmonary, positive pressure ventilation for > 7 days; renal, increase in serum creatinine > 2.0 mg/dL over baseline; hepatic, lactate dehydrogenase > 500 international units and total bilirubin > 3.0 mg/dL or serum transaminase level > 200 international units; hematopoietic, platelet count > 50 K or leukocyte count > 4.5 K, mortality, and costs. RESULTS No relationship between preoperative organ dysfunction, blood loss, or operative time and postoperative organ dysfunction or mortality was seen; however, cross-clamp times > 40 minutes were associated with a significantly greater incidence of pulmonary (59%), renal (47%), hepatic (35%), and hematopoietic (47%) dysfunction. In addition, multiple-organ dysfunction (> 2 organ systems) was more common after > 40 minutes of visceral ischemia and led to significantly greater overall hospital ($88,465 + $76,155 vs. $41,782 + $31,244) and intensive care unit ($26,726 + $28,256 vs. $11,234 + $12,146) costs (p < 0.01, Mann-Whitney U test). Mortality associated with leukopenia was 67% compared with 4% without leukopenia (p < 0.01). CONCLUSION Increasing durations of acute visceral ischemia led to significant multiple organ dysfunction after TAAA repair. Methods of limiting visceral ischemia or the systemic effects of visceral ischemia may decrease both the morbidity and mortality and the overall hospital cost associated with this procedure.
Making the best use of available evidence: the case of new generation antidepressants

In this issue of Evidence-Based Mental Health , Gartlehner and Gaynes1 comment (see page 98) on our recently published systematic review2 that investigated the comparative efficacy and acceptability of 12 new generation antidepressants (see page 107) . In their view, methodological shortcomings limit the validity of our results and the conclusions reached. In this commentary, our aim is to explain the rationale for doing this systematic review, outline its main findings and address the points raised by Gartlehner and Gaynes.1 Scientific debate can illuminate and clarify complex analyses and we are, therefore, delighted to respond to their critique. While we consider that some of the issues raised are substantive and merit reasoned response, we also believe that some of their criticisms seem rather overstated. We understand that Gartlehner and Gaynes too have published an analysis comparing antidepressants and we note that this is now the third occasion on which they have published similar criticisms of our work.3 ,4 In most countries, demonstration of a difference against placebo, and not against an active comparator, makes a new drug eligible for registration. The European Medicines Agency, for example, is willing to evaluate new antidepressants in the absence of comparison with active existing treatments.5 In situations where no (or a few) active treatments are available, this may not be important. In the field of antidepressants, however, where many potentially effective agents are already available, this process has serious implications. The approval of a new antidepressant as effective and safe in comparison solely with placebo allows the marketing of new drugs that may, in fact, be potentially more effective, similarly effective or even less effective than others currently in use. Many antidepressants have never been directly compared with each other. The picture is further complicated by …
FHIT Doubts are Clear Now

The fragile histidine triad (FHIT) gene is a bonafide tumor-suppressor gene present on the short arm of chromosome 3 and its loss of function has been evaluated in different types of cancers. Loss of heterozygosity at various sections of the FHIT gene and the methylation analysis of the promoter region showed that it is one of the important and preliminary genetic alterations in the cell, and its restoration in the cell line or nude mice suppresses tumorigenicity. Current research on the FHIT gene has depicted that Fhit interacts with different proteins through different pathways in the nucleus, mitochondria, and cytoplasm, directing the cell to apoptosis.
Modeled gravitational unloading triggers differentiation and apoptosis in preosteoclastic cells

Gravity acts permanently on organisms as either static or dynamic stimulation. Understanding the influence of gravitational and mechanical stimuli on biological systems is an intriguing scientific problem. More than two decades of life science studies in low g, either real or modeled by clinostats, as well as experimentation with devices simulating different types of controlled mechanical stimuli, have shown that important biological functions are altered at the single cell level. Here, we show that the human leukemic line FLG 29.1, characterized as an osteoclastic precursor model, is directly sensitive to gravitational unloading, modeled by a random positioning machine (RPM). The phenotypic expression of cytoskeletal proteins, osteoclastic markers, and factors regulating apoptosis was investigated using histochemical and immunohistochemical methods, while the expression of the corresponding genes was analyzed using RT‐PCR. A quantitative bone resorption assay was performed. Autofluorescence spectroscopy and imaging were applied to gain information on cell metabolism. The results show that modeled hypogravity may trigger both differentiation and apoptosis in FLG 29.1 cells. Indeed, when comparing RPM versus 1 × g cultures, in the former we found cytoskeletal alterations and a marked increase in apoptosis, but the surviving cells showed an osteoclastic‐like morphology, overexpression of osteoclastic markers and the ability to resorb bone. In particular, the overexpression of both RANK and its ligand RANKL, maintained even after return to 1 × g conditions, is consistent with the firing of a differentiation process via a paracrine/autocrine mechanism. J. Cell. Biochem. 98: 65–80, 2006. © 2005 Wiley‐Liss, Inc.
First observations of the second solar spectrum with spatial resolution at the Lunette Jean Rösch

Context. A new polarimeter has been installed at the focus of the 50 cm refractor of the Lunette Jean R¨ osch (LJR), previously known as Turret Dome, Pic du Midi, France, for spectroscopic observations of weak solar magnetic fields. Fields can be derived through the Hanle effect from the depolarization of the second solar spectrum (i.e. the linearly polarized spectrum at the limb). Aims. We present the first observations with spatial resolution based on the new device performed with the large 8 m Echelle spectrograph, or recorded in imagery mode through narrow band filters. The observations started in April 2004, especially in the blue part of the spectrum where our instrumentation has a particularly good efficiency. The capabilities and the characteristics of the new instrument are briefly described. We observed several lines of the second solar spectrum with the slit of the spectrograph orthogonal to the limb to study the polarization as a function of limb distance (which is related to altitude in the atmosphere), and several spectral windows in imagery to determine the average continuum polarization. Methods. The polarimeter uses Nematic Liquid Crystal (NLC) technology at the primary focus of the refractor, in spectroscopic or imagery mode. Results. A continuous polarization profile through the limb is presented for the photospheric SrI 460.7 nm line, the low chromospheric BaII 455.4 nm line, and the CaI 422.7 nm line within a distance of 120 ′′ , together with measurements of the mean continuum polarization obtained in imagery mode. Preliminary results of the polarization of the SrI 460.7 nm line are also shown at 40 ′′ from the limb, as a function of the brightness of structures visible in the continuum (granulation). They reveal a tendency for the polarization to be weaker in dark features (intergranules) than in bright ones (granules), suggesting a stronger magnetic field in intergranular lanes. Finally an example of the enigmatic and weak polarization signal in the core of the NaD1 589.6 nm line is presented. Conclusions. Some aspects of the spatial variation of the polarization with respect to the granulation pattern require further investigation at higher spatial resolution.
Next-generation sequencing as a tool to quickly identify causative EMS-generated mutations

The advent of next generation sequencing has influenced every aspect of biological research. Many labs are now using whole genome sequencing in Arabidopsis thaliana as a means to quickly identify EMS-generated mutations present in isolated mutants. Following identification of these mutations, examination of T-DNA insertional alleles defective in candidate genes or complementation of the mutant phenotype with a wild type copy of candidate genes can be used to verify which mutation is causative for the phenotype of interest. Here, we discuss the benefits and pitfalls of using this method to identify mutations underlying phenotypes.
Incidence of foot and skin lesions in nursing piglets and their association with behavioural activities

A total of 356 piglets from one farm were examined for foot and skin lesions every day for the first 10 days after birth, and then on altemate days until they were weaned. Over a period of 24 days 100 per cent of the after birth, and then on altemate days until they were weaned. Over a period of 24 days 100 per cent of the piglets examined developed sole bruising, and 49-1 per cent developed sole erosions. Sole bruising lasted for an average of 13 days and sole erosions for seven days. At the beginning of the study, a higher proportion of piglets had mild sole bruising; from three to nine days of age piglets had moderate sole bruising but from days 10 to 20 mild bruising was again observed more frequently. Skin lesions were observed on the carpal aspect of the front limbs; 60.9 per cent of the piglets developed skin abrasions, 70.7 per cent developed healed wounds and 90 per cent developed hairless patches. The skin abrasions lasted on average for six days, the healed wounds for five days and the hairless patches for eight days. Piglets which developed sole bruising and/or sole erosions on the first day of life were significantly heavier than those which did not. Continuous observations of the piglets' behaviour during the first six days of life showed that sole bruising increased as the total time spent in the creep area or lying near the sow on the solid floor increased. During the first three days of life skin abrasions increased as the total time spent lying in the creep area increased. There was a positive correlation between the total time piglets spent suckling and the incidence of carpal skin abrasions between four and six days of age. Piglets with sole bruising, sole erosions or carpal skin abrasions spent less time during the day in ‘other’ activities such as walking, playing or fighting.
Survival Analysis of Pseudomyxoma Peritonei Patients Treated by Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy

Objective:To evaluate the survival of patients with pseudomyxoma peritonei (PMP) treated by cytoreductive surgery and intraoperative hyperthermic intraperitoneal chemotherapy (HIPEC), and to identify factors with prognostic value. Summary Background Data:PMP is a clinical syndrome characterized by progressive intraperitoneal accumulation of mucous and mucinous implants, usually derived from a ruptured mucinous neoplasm of the appendix. Survival is dominated by pathology. Methods:A total of 103 patients (34 men and 69 women) treated at The Netherlands Cancer Institute between 1996 and 2004 were identified. Survival was calculated from date of initial treatment and corrected for a second procedure. PMP was pathologically categorized into disseminated peritoneal adenomucinosis (DPAM), peritoneal mucinous carcinomatosis (PMCA), and an intermediate subtype (PMCA-I). Clinical and pathologic factors were analyzed to identify their prognostic value for survival. Results:Median follow-up was 51.5 months (range, 0.1–99.5 months). Recurrence developed in 44%. A second procedure for recurrence was performed in 11 patients. The median disease-free interval was 25.6 months (95% confidence interval [CI], 14.8–43.6 months). The 3-year and 5-year disease-free survival probability was 43.6% (95% CI, 34.4%–55.2%) and 37.4% (95% CI, 28.2%–49.5%), respectively. The disease-specific 3-year and 5-year survival probability was 70.9% (95% CI, 62.0%–81.2%) and 59.5% (95% CI 48.7%–72.5%), respectively. Factors associated with survival were pathological subtype, completeness of cytoreduction, and degree and location of tumor load (P < 0.05). The main prognostic factor, independently associated with survival, was the pathologic subtype (P < 0.01). Conclusion:Cytoreductive surgery in combination with intraoperative HIPEC is a feasible treatment strategy for PMP in terms of survival. The pathologic subtype remains the dominant factor in survival. Patients should be centralized to improve survival by a combination of surgical experience and adequate patient selection.
Classification of Aerial Photogrammetric 3D Point Clouds

Abstract. We present a powerful method to extract per-point semantic class labels from aerial photogrammetry data. Labelling this kind of data is important for tasks such as environmental modelling, object classification and scene understanding. Unlike previous point cloud classification methods that rely exclusively on geometric features, we show that incorporating color information yields a significant increase in accuracy in detecting semantic classes. We test our classification method on three real-world photogrammetry datasets that were generated with Pix4Dmapper Pro, and with varying point densities. We show that off-the-shelf machine learning techniques coupled with our new features allow us to train highly accurate classifiers that generalize well to unseen data, processing point clouds containing 10 million points in less than 3 minutes on a desktop computer.
Organic and inorganic nitrogen amendments to soil as nematode suppressants.

Inorganic fertilizers containing ammoniacal nitrogen or formulations releasing this form of N in the soil are most effective for suppressing nematode populations. Anhydrous ammonia has been shown to reduce soil populations of Tylenchorhynchus claytoni, Helicotylenchus dihystera, and Heterodera glycines. The rates required to obtain significant suppression of nematode populations are generally in excess of 150 kg N/ha. Urea also suppresses several nematode species, including Meloidogyne spp. , when applied at rates above 300 kg N/ha. Additional available carbon must be provided with urea to permit soil microorganisms to metabolize excess N and avoid phytotoxic effects. There is a direct relation between the amount of "protein" N in organic amendments and their effectiveness as nematode population suppressants. Most nematicidal amendments are oil cakes, or animal excrements containing 2-7% (w:w) N; these materials are effective at rates of 4-10 t/ha. Organic soil amendments containing mucopolysaccharides (e.g., mycelial wastes, chitinous matter) are also effective nematode suppressants.
CHANGEMENTS CLIMATIQUES ET VARIATIONS DES ECOULEMENTS EN AFRIQUE OCCIDENTALE ET CENTRALE, DU MENSUEL A L'INTERANNUEL

RESUME Les ecoulements depuis la facade atlantique de l'Afrique sont analyses sur la periode 1951-1989. La repartition regionale des volumes ecoules annuels et mensuels est quantifiee. Les apports sont globalement moyens durant la decennie 1950, largement excedentaires entre 1961 et 1970 et deficitaires depuis. Des disparites regionales existent, en particulier celles du couple Afrique occidentale-Afrique equatoriale, mais les sequences deficitaires de 1972-1973 et 1982-1984 apparaissent dans toutes les series.L'apport annuel moyen a l'Atlantique du Senegal au Congo est de 2660 milliards de m'. an". En 1962 l'apport supplementaire est de 610 milliards (23%); en 1983 le deficit est de 900 milliards (34%). Un exemple d'etude de fleuve est fourni par l'analyse des debits de l'Ogooue (Gabon), dont 1'occurence et l'intensite des crues sont profondement modifies depuis 1970, traduisant une modification climatique recente a Pequateur.