Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Protein Expression in Human Muscle Biopsies

Using immunohistochemistry in diagnosing neuromuscular diseases is meant to enhance the diagnostic yield in two ways. The first application aims at visualizing molecules which are developmentally, neurally, and/or immunologically regulated and not expressed by normal muscle. They are upregulated in pathological conditions and may help assign a given muscular biopsy to one of the main diagnostic entities (muscular dystrophies, inflammatory myopathy, neurogenic atrophy). In the past, muscle‐specific molecules with a defined expression pattern during fetal myogenesis served as antigens, with the rationale that the developmental program was switched on in new fibers. Recently, myofibers in diseased muscle are thought of as targets of stimuli which are released by macrophages in muscular dystrophy, by lymphocytes in inflammatory myopathies, or by a lesioned peripheral nerve in neurogenic atrophies. This has somewhat blurred the borders between the diagnostic groups, for certain molecules, e.g. cytokines, may be upregulated after experimental necrotization, denervation, and also in inflammatory myopathies. In the second part of this review we summarise the experiences of a Centre in the North of England that specialises in the diagnosis and clinical support of patients with muscular dystrophy. Emphasis is placed on the use of protein expression to guide mutation analysis, particularly in the limb‐girdle muscular dystrophies (a group of diseases that are very difficult to differentiate on clinical grounds alone). We confirm that genetic analysis is essential to corroborate the results of protein analysis in certain conditions (particularly in calpainopathy). However, we conclude that analysing biopsies for abnormal protein expression is very useful in aiding the decision between alternative diagnoses.
Estimating the Aboveground Dry Biomass of Grass by Assimilation of Retrieved LAI Into a Crop Growth Model

This study presents a method to assimilate leaf area index (LAI) retrieved from MODIS data using a physically based method into a soil-water-atmosphere-plant (SWAP) model to estimate the aboveground dry biomass of grass in the Ruoergai grassland, China. The assimilation method consists of reinitializing the model with optimal input parameters that allow a better temporal agreement between the LAI simulated by the SWAP model and the LA! retrieved from MODIS data. The minimization is performed by a four-dimensional variational data assimilation (4D-VAR) algorithm but which is challenged by the development of the adjoint model. The automatic differentiation (AD) technique is thus used to provide the adjoint model at the level of computer language codes. After the re-initialization, the simulated aboveground dry biomass value is compared with ground measurements taken in early August2013. The results show that the biomass can be estimated with highly satisfactory accuracy level through the assimilation method with R2(the deterministic coefficient) = 0.73 and RMSE(root-mean-square error) = 617.94 kg ha-1. The accuracy is further improved when the newly derived RMSELAI values are used as observation errors in the assimilation process, with R2 = 0.76 and RMSE = 542.52 kgha-1. Both assimilation strategies yield a significant improvement in SWAP model accuracy with respect to no significant correlation obtained when the SWAP model is run alone with constant values of the input parameters employed for the whole area. The validity of the 4D-VAR method for biomass estimation is well demonstrated.
Application of computer-supported content analysis on Twitter: a case study on Swiss national media criticism

Media and media content are of considerable social relevance. However, the systematic and automated extraction of media content is hardly a subject in the communication and media studies. This also applies to the potential use of computer-assisted content analysis as an alternative or complement to manual coding in a media science context. My project aims to address this research gap and reduce labor-intensive processes by using machine learning methods and pooled computing resources to automatically extract topic related data from Twitter. As research topic the project intents to analyze the status quo of Swiss national media-criticism. This project combines the two research fields computer linguistics applied to media studies and examines the extent to which an automated process using a Naïve-Bayes algorithm can adequately identify content containing Swiss national media-criticism. To answer this question the results are validated by means of manual content analysis.
Is optimising gout treatment the key to closing the mortality gap in gout patients?

With great interest we read the extended report of Fisher et al 1 on the unclosing premature mortality gap in gout and we congratulate the authors on their extensive work. In their population-based cohort study, the authors found that among the patients with gout, the level of premature mortality remained unimproved over the past 16 years. However, there are a few issues that, in our opinion, merit attention concerning the conclusions that were drawn from the data: 1. The authors hypothesise that proper urate control could have cardiovascular–metabolic–renal benefits, and thus optimising gout treatment would reduce mortality. However, the authors have chosen ‘all-cause mortality’ as their outcome, most likely because disease-related mortality was not available.2 In rheumatoid arthritis (RA), the main cause for premature mortality is cardiovascular death, with poor clinical RA status prognostic of premature mortality, and thus the closing mortality gap may very well be due to tighter disease …
Absence of HIV transmission from an infected orthopedic surgeon. A 13-year look-back study.

OBJECTIVE To determine the risk of human immunodeficiency virus (HIV) transmission from an HIV-infected orthopedic surgeon to patients undergoing invasive procedures. DESIGN Retrospective epidemiologic follow-up study. PARTICIPANTS A total of 2317 former patients on whom the orthopedic surgeon performed invasive procedures between January 1, 1978, and June 30, 1991 [corrected]. MAIN OUTCOME MEASURES HIV infection or death from an acquired immunodeficiency syndrome (AIDS)-defining tumor or opportunistic infection. RESULTS An orthopedic surgeon voluntarily withdrew from practice after testing positive for HIV. Testing for HIV was performed on 1174 former patients, representing 50.7% of patients on whom the orthopedic surgeon performed invasive procedures during the 13.5-year period. Patients were tested from each year and from each category of invasive procedure. All patients were HIV-negative by enzyme-linked immunosorbent assay. Two former patients reported known HIV infection prior to surgery. Review of AIDS case registries and vital records failed to detect cases of HIV infection among former surgical patients. The estimated cost of the initial patient notification and testing was $158,500. The patient notification and testing were conducted while maintaining the confidentiality of the orthopedic surgeon who was an active participant in the planning and execution of the study. CONCLUSIONS The risk of HIV transmission from an HIV-infected surgeon who adheres to recommended infection control practices is extremely low. Notification and HIV testing of former patients in this setting is both disruptive and expensive and is not routinely recommended.
Review article: current management of primary sclerosing cholangitis

The management of primary sclerosing cholangitis (PSC) is hindered by incomplete understanding of the pathogenesis of the disease and the lack of good prognostic models. Few large randomized controlled trials of drug therapy have been published. Best practice in the management of PSC is currently based therefore on careful interpretation of the available evidence, close observation of individual patients and clinical experience of the disease. Drug therapy is useful for alleviating symptoms. Ursodeoxycholic acid may slow progression of the disease and reduce the frequency of complications. Consensus is emerging on the issues of screening for the malignant complications of PSC and the indications for liver transplantation are becoming broader and encompassing the earliest stages of cholangiocarcinoma. In view of the rarity of the disease in the general population, large international collaborations to study PSC are necessary to provide clearer answers in areas of uncertainty, and these are now beginning to emerge.
Circulating vascular endothelial growth factor and the risk of cardiovascular events

Objective To investigate the relation of circulating concentrations of vascular endothelial growth factor (VEGF) for the risk of developing cardiovascular disease (CVD) in a large community-based sample. Methods We prospectively assessed the relation of circulating VEGF concentrations with the incidence of CVD among 3041 Framingham Heart Study participants (mean age 63.4±11.1 years, 59% women). Multivariable Cox proportional hazards models were estimated adjusting for standard risk factors to VEGF quartiles to incident CVD. Restricted cubic splines were used to examine the linearity of the association. Results After a mean follow-up of 8.8 (±2.8) years, 527 individuals experienced a first CVD event. Compared with participants in the first VEGF quartile, individuals in the second VEGF quartile had a 34% increased risk for future CVD (HR 1.34, 95% CI 1.03 to 1.74; p value=0.03) and individuals in third quartile had a 59% higher risk (HR 1.59; 95% CI 1.23 to 2.05, p value=0.0003). Individuals in the highest VEGF quartile had a similar cardiovascular risk as compared with those in the lowest VEGF quartile (HR 1.18, 95% CI 0.91 to 1.53, p value=0.21). Evaluation of restricted cubic splines confirmed the nonlinear, inverted U-shaped relation of serum VEGF and CVD events (p<0.0001 for model fit, p=0.006 for non-linearity). Conclusions Circulating VEGF concentrations exhibit a complex non-linear (inverted U-shaped) relation with the risk of developing CVD events, with the lowest risk experienced at the lower and upper end of the distribution. The underlying pathophysiological mechanisms remain to be elucidated.
Effects of oxytocin, machine stripping and milking rate on production loss of cows milked once a day

Summary The effect of treatments designed to improve the efficiency of milk removal and minimize loss of production in cows milked once a day (OAD) was assessed in short-term trials involving Friesian and Jersey cows. Trial 1 involved 80 cows and compared twice a day (TAD) milking with OAD milking with the administration of 20 i.u. of oxytocin (OX), OAD milking with udder massage before and during milking (OS) and no treatment during OAD milking (OC). The OX and OS groups had increased yields of milk and milk solids when treatments were applied, though yields were not restored to previous TAD levels. The percentage increase shown by OX cows was greater than that of OS cows for fat yield. The level of residual milk in the udder after milking was lower for the OX group than for the OAD and TAD controls. In Trial 2, 12 cows were subjected to fast or slow rates of milking OAD in each of two periods. Losses in milk, fat and protein yields averaged 9·1, 9·9 and 1·0% respectively. Increased rate of milking reduced milking time and time to let-down but did not affect response to OAD milking. The results showed that treatments that increased the evacuation of the udder during milking and decreased the level of residual milk reduced losses in production that occur on OAD milking. Increasing the rate of milking was ineffective in reducing losses on OAD milking.
Fabrication of Tapered Tip Fibers With a Controllable Cone Angle Using Dynamical Etching

Recently, optical fiber tips have been used in many scientific applications requiring a special tip with a predetermined cone angle. In this study, we have developed a new type of dynamic chemical etching for fabricating fiber tips which enables us to fabricate tips with predetermined cone angles. The fiber tips are fabricated by injecting or withdrawing hydrofluoric acid to the container in which the fiber is vertically inserted. By changing the flow rate of the acid injection or withdrawal, the height of the fiber in contact with the acid can be controlled. This method produces cone angles from 3° to 33°. Additionally, a model is proposed for this procedure which covers all the special cases and is in good agreement with the experimental results.
Clinical utility of the K-T cancellation test in a memory clinic population

ABSTRACT Background/Aim: The K-T cancellation test (K-T) has been validated as a measure of executive functions (EF) but its clinical utility has not yet been examined. This study aimed to validate K-T in a memory clinic setting by examining its capacity to discriminate older adults with normal cognition (NC) from those with mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Method: K-T was administered to 120 NC subjects, 146 patients with MCI, and 93 patients with AD. A one-way analysis of covariance was used to compare the correct cancellations of K-T between the groups. Linear regressions were run to identify significant demographic predictors of K-T for NC subjects and to determine the equation to calculate z scores for all subjects. The area under the curve (AUC), sensitivity (Se), specificity (Sp), and positive (PPV) and negative (NPV) predictive values were assessed to compare the diagnostic performance between K-T and the Mini-Mental State Examination (MMSE) for discrimination between NC subjects and patients with cognitive impairment. Results: After adjusting for age, education, and gender, the groups were significantly different from each other regarding the number of correct cancellations of K-T, F(2, 353) = 116.6, p < . 001, η2p = . 40. Compared to the NC group (Z = 0, SD = 1), the mean z score was –1.52 for the MCI group and –2.53 for the AD group, suggesting impaired performance for the patient groups. K-T showed a better diagnostic performance for discrimination between the NC subjects and the patients with MCI (AUC = .83; 95% CI [.79, .88]; Se = .79; Sp = .74; PPV = .79; NPV = .74), compared to that of MMSE (AUC = .74, 95% CI [.68, .80]; Se = .68; Sp = .73; PPV = .79; NPV = .64). Conclusion: The K-T cancellation test showed a good diagnostic performance in discriminating cognitively normal older adults from cognitively impaired patients. Our findings support the clinical utility of K-T in geriatric neuropsychological assessment for detection of early cognitive impairment.
Monoclonal antibody 18B8, which detects synapse-associated antigens, binds to ganglioside GT3 (II3 (NeuAc)3LacCer).

By immunofluorescence, mouse monoclonal antibody 18B8 detects developmentally regulated antigens in chick neural retina. In older embryos and in adults these antigens are localized in discrete laminae within the inner and outer synaptic layers. The antibody binds to several gangliosides that undergo both qualitative and quantitative changes during neuronal development (Grunwald, G.B., Fredman, P., Magnani, J.L., Trisler, D., Ginsburg, V., and Nirenberg, M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 4008-4012). The simplest of these gangliosides was isolated from lipid extracts of 10-day chick embryonic retinas by DEAE-Sepharose and silicic acid column chromatography. About 300 micrograms was obtained from 9.3 g (wet weight) of retina. The isolated ganglioside was identified as GT3 by enzymatic analysis and by a comparison of its properties with the authentic ganglioside. By immunostaining thin-layer chromatograms with antibody 18B8, GT3 was detected in gangliosides from human neural tissue including cerebellum, optic nerve, and spinal cord, but not in gangliosides from human liver, pancreas, small intestine, adrenals, thyroid, or erythrocytes. GT3 was also found in five of seven human melanoma cell lines.
Relationship Between Lateral Inhibitory Connections and the Topography of the Orientation Map in Cat Visual Cortex

The functional and structural topography of lateral inhibitory connections was investigated in visual cortical area 18 using a combination of optical imaging and anatomical tracing techniques in the same tissue. Orientation maps were obtained by recording intrinsic signals in regions of 8.4–19 mm2. To reveal the inhibitory connections provided by large basket cells, biocytin was iontophoretically injected at identified orientation sites guided by the pattern of surface blood vessels. The axonal and dendritic fields of two retrogradely labelled large basket cells were reconstructed in layer III. Their axonal fields extended up to 1360 μm from the parent somata. In addition to single basket cells, the population of labelled basket cell axons was also studied. For this analysis anterogradely labelled basket axons running horizontally over 460–1280 μm from the core of an injection site in layer III were taken into account. The distribution of large basket cell terminals according to orientation preferences of their target regions was quantitatively assessed. Using the same spatial resolution as the orientation map, a frequency distribution of basket cell terminals dependent on orientation specificity could be derived. For individual basket cells, the results showed that, on average, 43% of the terminals provided input to sites showing similar orientation preferences (±30°) to those of the parent somata. About 35% of the terminals were directed to sites representing oblique‐orientation [±(30–60)°], and 22% of them terminated at cross‐orientation sites [±(60–90)°]. Furthermore, the possible impact of large basket cells on target cells at different distances and orientation preferences was estimated by comparing the occurrence of orientation preferences with the occurrence of basket terminals on the distance scale. It was found that a basket cell could elicit iso‐orientation inhibition with a high impact between 100–400 and 800–1200 μm strong cross‐orientation inhibition at ∼400–800 μm, and oblique‐orientation inhibition between 300–500 and 700–900 μm from the parent soma. The non‐isotropic topography of large basket axons suggests a complex function for this cell class, possibly including inhibition related to orientation and direction selectivity depending on the location of the target cells and possible target selectivity.
A multiple process solution to the logical problem of language acquisition

Many researchers believe that there is a logical problem at the centre of language acquisition theory. According to this analysis, the input to the learner is too inconsistent and incomplete to determine the acquisition of grammar. Moreover, when corrective feedback is provided, children tend to ignore it. As a result, language learning must rely on additional constraints from universal grammar. To solve this logical problem, theorists have proposed a series of constraints and parameterizations on the form of universal grammar. Plausible alternatives to these constraints include: conservatism, item-based learning, indirect negative evidence, competition, cue construction, and monitoring. Careful analysis of child language corpora has cast doubt on claims regarding the absence of positive exemplars. Using demonstrably available positive data, simple learning procedures can be formulated for each of the syntactic structures that have traditionally motivated invocation of the logical problem. Within the perspective of emergentist theory (MacWhinney, 2001), the operation of a set of mutually supportive processes is viewed as providing multiple buffering for developmental outcomes. However, the fact that some syntactic structures are more difficult to learn than others can be used to highlight areas of intense grammatical competition and processing load.
Differential Diagnosis of Chronic Total Occlusive and Subtotal Occlusive Disease of the Lower Extremity Arteries Using Reverse Attenuation Gradient Sign on CT Angiography.

OBJECTIVE The purpose of this study is to evaluate the diagnostic usefulness of the reverse attenuation gradient sign in occlusive lower extremity arterial disease through CT angiography (CTA). MATERIALS AND METHODS This study sample enrolled 45 men and eight women in the chronic total occlusion group and 30 men and seven women in the subtotal occlusion group. Luminal CT attenuation (in Hounsfield units) was measured at three points from the end of the occlusion site to the first collateral vessel's insertion point. We also used Hounsfield units to measure the CT attenuation of the opposite side artery at the same level in a similar manner. We compared each value using the Mann-Whitney U test. RESULTS The absolute value of the mean differences in the Hounsfield units among the proximal, middle, and distal portion of chronic total occlusions were higher than those of subtotal occlusions, and this result was statistically significant (p < 0.001). The mean ratios of the Hounsfield units (Hounsfield units of the stenosed lumen divided by Hounsfield units of the opposite normal lumen) of the proximal portion of chronic total occlusions were statistically significantly lower than those of subtotal occlusions. CONCLUSION The reverse attenuation gradient sign can be applied to the lower extremity arteries and can be helpful for differential diagnosis of chronic total occlusions from subtotal occlusions using CTA.
Functional adaptations of the coronary microcirculation to anaemia in fetal sheep

In fetuses, chronic anaemia stimulates cardiac growth; simultaneously, blood flow to the heart muscle itself is increased, and reserve blood flow capacity of the coronary vascular bed is preserved. Here we examined functional adaptations of the capillaries and small blood vessels responsible for delivering oxygen to the anaemic fetal heart muscle using contrast‐enhanced echocardiography. We demonstrate that coronary microvascular flux rate doubled in anaemic fetuses compared to control fetuses, both at rest and during maximal flow, suggesting reduced microvascular resistance consistent with capillary widening. Cardiac fractional microvascular blood volume was not greater in anaemic fetuses, suggesting that growth of new microvascular vessels does not contribute to the increased flow per volume of myocardium. These unusual changes in microvascular function during anaemia may indicate novel adaptive strategies in the fetal heart.
An outbreak of canine aflatoxicosis in Gauteng Province, South Africa.

Sporadic outbreaks of aflatoxicosis occur in dogs when they consume contaminated dog food. During 2011, low-cost brands of pelleted dog food were contaminated with very high concentrations of aflatoxins. Approximately 100 dogs were presented to the Onderstepoort Veterinary Academic Hospital. Clinically, the dogs were depressed to collapsed and icteric, with haematemesis, melaena and haematochezia. The most common pathological findings were icterus, gastro-enterorrhagia and hepatosis. On histopathological examination, fatty hepatosis and bile duct proliferation were observed. A consistent, very characteristic finding was the presence of a blue-grey granular material within the bile ducts. A total of 124 samples of the dog food fed to the affected dogs was analysed to determine aflatoxin concentrations. Concentrations ranged from below the limit of quantification (< 5 μg/kg) to 4946 μg/kg and six samples were submitted to determine the ratio of aflatoxins in the feed. It is estimated that well over 220 dogs died in the Gauteng Province of South Africa as a result of this aflatoxin outbreak.