Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting Diagnostic Knowledge from MedLine Plus: A Comparison between MetaMap and cTAKES Approaches

The development of diagnostic decision support systems (DDSS) requires having a reliable and consistent knowledge base about diseases and their symptoms, signs and diagnostic tests. Physicians are typically the source of this knowledge, but it is not always possible to obtain all the desired information from them. Other valuable sources are medical books and articles describing the diagnosis of diseases, but again, extracting this information is a hard and time-consuming task. In this paper we present the results of our research, in which we have used Web scraping, natural language processing techniques, a variety of publicly available sources of diagnostic knowledge and two widely known medical concept identifiers, MetaMap and cTAKES, to extract diagnostic criteria for infectious diseases from MedLine Plus articles. A performance comparison of MetaMap and cTAKES is also presented.
Acidogenesis and Two‐Phase Codigestion of Fats, Oils, and Greases and Municipal Biosolids

Acidogenic codigestion of fats, oils, and greases (FOG) was studied using suspended growth sludge digesters operated as batch fed reactors that were fed twice daily. The digesters were maintained at a 2‐day retention time and at 37 °C to mimic the acid phase of an acid‐gas digestion system. As FOG loading rates increased, volatile fatty acid (VFA) production was found to increase, although the percentage of VFA production compared to theoretical values decreased exponentially to just 20% at the highest loading rates. FOG matter was found to have accumulated in the reactor vessel in semi‐solid balls that floated near the liquid surface. Two‐phase codigestion of FOG was studied at 37 °C using Continuously Stirred Tank Reactors (CSTRs) as acid phase digesters (APD) operated with 2‐day retention times, followed by gas phase digesters (GPD) with 15‐day retention times. The two‐phase systems were compared by FOG addition to the APD versus GPD. FOG addition to the APD resulted in 88% destruction of LCFAs, whereas FOG addition to the GPD resulted in 95% destruction of LCFAs. Accumulated LCFAs were found in the APD receiving FOG and were primarily composed palmitic acid (16:0), followed by oleic acid (18:1) and stearic acid (18:0).
Growth Hormone Response to Clonidine in Obsessive-Compulsive Patients

Summary We have observed a lesser growth hormone response to intravenous clonidine administration in nine obsessive-compulsive disorder patients meeting research diagnostic criteria than in nine matched controls. The obsessive-compulsive disorder patients had higher plasma free 3-methoxy-4-hydroxyphenylglycol and plasma norepinephrine levels before clonidine than the controls. As blunted growth hormone responses to clonidine are also characteristic of affective disorder patients, these results support other observations of a psychobiologic affinity between these two groups and are also compatible with an association between increased presynaptic noradrenergic activity and decreased post-synaptic receptor responsiveness.
Carbohydrate analysis of glycoprotein hormones.

Complete carbohydrate composition analysis of glycoprotein hormones, their subunits, and oligosaccharides isolated from individual glycosylation sites can be accomplished using high-pH anion-exchange chromatography combined with pulsed amperometric detection. Neutral and amino sugars are analyzed from the same hydrolyzate by isocratic chromatography on a Dionex CarboPAC PA1 column in 16 mM NaOH. Sialic acid is quantified following mild hydrolysis conditions on the same column in 150 mM sodium acetate in 150 mM NaOH. Ion chromatography on a Dionex AS4A column in 1.8 mM Na(2)CO(3)/1.7 mM NaHCO(3); postcolumn, in-line anion micromembrane suppression; and conductivity detection can be used to quantify sulfate, a common component of pituitary glycoprotein hormone oligosaccharides. Mass spectrometric analysis before and after elimination of oligosaccharides from a single glycosylation site can provide an estimate of the average oligosaccharide mass, which facilitates interpretation of oligosaccharide composition data. Following release by peptide N-glycanase (PNGase) digestion and purification by ultrafiltration, oligosaccharides can be characterized by a high-resolution oligosaccharide mapping technique using the same equipment employed for composition analysis. Oligosaccharide mapping can be applied to the entire hormone, individual subunits, or individual glycosylation sites by varying PNGase digestion conditions or substrates. Oligosaccharide release by PNGase is readily monitored by SDS-PAGE. Site-specific deglycosylation can be confirmed by amino acid sequence analysis. For routine isolation of oligosaccharides, addition of 2-aminobenzamide at the reducing terminus facilitates detection; however, the oligosaccharide retention times are altered. Composition analysis is also affected as the 2-aminobenzamide-modified GlcNAc peak overlaps the fucose peak.
Economics of biosecurity across levels of decision-making: a review

Biosecurity is a concept that has important economic, social, ecological and health-related dimensions. By biosecurity we mean protection of production, ecosystems, health and the social infrastructure from external threats caused by pests, pathogens and diseases of various forms and origins. The fact that more goods, transport platforms and people are moving around the globe at increasing speeds provides unforeseen possibilities for rapid spread of different types of organisms. This is exacerbated by changes in the production structures and climate. As a result, both the benefits and the risks of changes in the food system cross borders more often, leading to an increased demand for biosecurity policies. Economics can be related to biosecurity in at least three fundamental ways. First, many of the ultimate or proximate causes of bioinvasions create economic welfare. Second, bioinvasions result in various types of impacts, many of which are economic by nature — or at least may be measured in economic terms. Third, the negative impacts of invasions or their probability of occurrence can often be either avoided or reduced. These biosecurity policies themselves have economic implications, which often may be quite different from those caused by the biological hazard itself. A few reviews of separate components of economics of biosecurity exist, but there have been no attempts to review the big picture. Instead, the previous reviews have concentrated on different components of biosecurity such as invasive species or animal diseases. Our aim is to look at the issue in broad terms, draw some commonalities from the research conducted, and identify areas in which economic analyses have primarily been conducted and in which areas there remains work to do. The review includes about 230 studies from all areas of biosecurity up to the year 2008. The review finds that study of economics of biosecurity is growing steadily, but is still relatively concentrated on narrow questions, few countries, few species/diseases and few journals.
A Perceptually Adaptive QIM Scheme for Efficient Watermark Synchronization

SUMMARY This study presents an adaptive quantization index modulation scheme applicable on a small audio segment, which in turn allows the watermarking technique to withstand time-shifting and cropping attacks. The exploitation of auditory masking further ensures the robustness and imperceptibility of the embedded watermark. Experimental results conﬁrmed the e ﬃ cacy of this scheme against common signal processing attacks.
Genetic susceptibility to acute lung injury

ObjectiveTo review the complex interactions of markers of genetic susceptibility for critical illness and acute lung injury. These may affect the responses of critically ill patients to acute lung injury and acute respiratory distress syndrome and may affect outcome. Data Sources and Study SelectionPublished research and review articles related to genetic factors associated with susceptibility to critical illnesses and pulmonary disease. Data Extraction and SynthesisCritical illness in adults often is followed by acute lung injury, a phenomenon of acute diffuse lung inflammation. Physicians have long known that each patient responds differently to drugs and has a different risk for a particular event or outcome. Now, there is some evidence that cellular and humoral immune responses are subject to polymorphic genetic control, which explains the well-known diversity of clinical manifestations and outcomes in critically ill patients with the same disease. By revealing altered expression of relatively few genes involved in the responses to lung injury and repair, some investigators have found that these responses, and susceptibility to acute lung injury, are heritable. In the last 5 yrs, we have discovered that an individual’s risks and cellular responses can be related to his or her own unique DNA. ConclusionsThe search for an association between functional variants of a gene and clinical phenotype may help to identify key pathophysiological processes of disease. In the future, we will know much about which therapy is best for each individual patient in the intensive care unit.
Black-box modeling of an ultra-precision positioning system using time series analysis

It is important to construct a precise model for the ultra-precision positioning system before designing the controller. Based on the step response of the system, first the experimental data is preprocessed, such as creating a uniform sampling rate by using interpolation, removing the noise with wavelet decomposition and deconstruction; then, the experimental data is divided into two parts: the transient part and the steady-state part, and the model is identified using time series analysis in both parts. An auto-regressive with exogenous (ARX) model is constructed and validated by analyzing the residuals in the transient part. In the steady-state part, the trend of an exponential form and a triangle form is removed from the data, and then an AR model is constructed for the residuals. The conclusion is drawn that the ARX model corresponds with the original model well and some nonlinearity exists in the system.
A novel approach for anomaly detection in data streams: Fuzzy-statistical detection mode

Anomalies are subsequences that exhibit departures from normal state of operation. In this paper, to solve the problems of unknown data distribution, control limit determination, multiple parameters, training data and fuzziness of 'anomaly', a self-adaptive and unsupervised model is developed for finding anomalies in data streams. A salient feature is a synergistic combination of both statistical and fuzzy set-based techniques. Anomaly detection problem is viewed as a certain statistical hypothesis testing which is realized in an unsupervised mode. At the same time, 'anomaly' is a much more complex concept and as such can be described with fuzzy set theory. Fuzzy sets bring a facet of robustness to the overall scheme and play an important role in the successive step of hypothesis testing. Because of the fuzzification, parameters determination is self-adaptive and no parameter needs to be specified by the user, what's more, there is no need to consider the data distribution in statistical hypothesis testing in this paper. The approach is validated with a number of experiments, which help to quantify the performance of constructed algorithm.
DETECTION AND EXTRACTION FROM VIDEOS USING ANN BASED NETWORK

With fast intensification of existing multimedia documents and mounting demand for information indexing and retrieval, much endeavor has been done on extracting the text from images and videos. The prime intention of the projected system is to spot and haul out the scene text from video. Extracting the scene text from video is demanding due to complex background, varying font size, different style, lower resolution and blurring, position, viewing angle and so on. In this paper we put forward a hybrid method where the two most well-liked text extraction techniques i.e. region based method and connected component (CC) based method comes together. Initially the video is split into frames and key frames obtained. Text region indicator (TRI) is being developed to compute the text prevailing confidence and candidate region by performing binarization. Artificial Neural network (ANN) is used as the classifier and Optical Character Recognition (OCR) is used for character verification. Text is grouped by constructing the minimum spanning tree with the use of bounding box distance.
Transcription from a murine T-cell receptor V beta promoter depends on a conserved decamer motif similar to the cyclic AMP response element

We identified a regulatory region of the murine V beta promoter by both in vivo and in vitro analyses. The results of transient transfection assays indicated that the dominant transcription-activating element within the V beta 8.3 promoter is the palindromic motif identified previously as the conserved V beta decamer. Elimination of this element, by linear deletion or specific mutation, reduced transcriptional activity from this promoter by 10-fold. DNase I footprinting, gel mobility shift, and methylation interference assays confirmed that the palindrome acts as the binding site of a specific nuclear factor. In particular, the V beta promoter motif functioned in vitro as a high-affinity site for a previously characterized transcription activator, ATF. A consensus cyclic AMP response element (CRE) but not a consensus AP-1 site, can substitute for the decamer in vivo. These data suggest that cyclic AMP response element-binding protein (ATF/CREB) or related proteins activate V beta transcription.
Apolipoprotein E4 in Macrophages Enhances Atherogenesis in a Low Density Lipoprotein Receptor-dependent Manner*

Apolipoprotein E (apoE) and the low density lipoprotein receptor (LDLr) are well recognized determinants of atherosclerosis. In addition to hepatocytes, where both are highly expressed and contribute to plasma lipoprotein clearance, they are expressed in vascular cells and macrophages. In this study, we examined the effects of human apoE isoforms and LDLr levels in atherogenic pathways in primary macrophages ex vivo and atherosclerosis development after bone marrow transfer in vivo using mice expressing human apoE isoforms and different levels of LDLr expression. Increases in LDLr expression significantly increased cholesterol delivery into macrophages in culture, and the effects were more prominent with lipoproteins containing apoE4 than those containing apoE3. Conversely, increased LDLr expression reduced cholesterol efflux in macrophages expressing apoE4 but not in macrophages expressing apoE3. Furthermore, apoE3 protected VLDL from oxidation in vitro more than did apoE4. In LDLr-deficient mice expressing the human apoE4 isoform, Apoe4/4 Ldlr–/–, the replacement of bone marrow cells with those expressing LDLr increased atherosclerotic lesions in a dose-dependent manner compared with mice transplanted with cells having no LDLr. In contrast, atherosclerosis in Apoe3/3 Ldlr–/– mice, expressing the human apoE3 isoform, did not differ by the levels of macrophage LDLr expression. Our results demonstrate that apoE4, but not apoE3, in macrophages enhances atherosclerotic plaque development in mice in an LDLr-dependent manner and suggests that this interaction may contribute to the association of apoE4 with an increased cardiovascular risk in humans.
Effects of Unpaired Nucleotides within HIV-1 Genomic Secondary Structures on Pausing and Strand Transfer*

Reverse transcriptase-mediated RNA displacement synthesis is required for DNA polymerization through the base-paired stem portions of secondary structures present in retroviral genomes. These regions of RNA duplex often possess single unpaired nucleotides, or “bulges,” that disrupt contiguous base pairing. By using well defined secondary structures from the human immunodeficiency virus, type 1 (HIV-1), genome, we demonstrate that removal of these bulges either by deletion or by introducing a complementary base on the opposing strand results in increased pausing at specific positions within the RNA duplex. We also show that the HIV-1 nucleocapsid protein can increase synthesis through the pause sites but not as efficiently as when a bulge residue is present. Finally, we demonstrate that removing a bulge increases the proportion of strand transfer events to an acceptor template that occur prior to complete replication of a donor template secondary structure. Together our data suggest a role for bulge nucleotides in enhancing synthesis through stable secondary structures and reducing strand transfer.
Popeye Sign After Tenotomy Versus Tenodesis: Letter to the Editor

Dear Editor: With great interest we have read the article of Cho and colleagues. The authors concluded that both tenotomy and tenodesis are equally effective for the treatment of long head biceps lesions associated with arthroscopic rotator cuff repair. They found no significant effect on clinical outcome as measured by the Constant score, no significant effect on the University of California, Los Angeles (UCLA) score, and no significant difference in the overall incidence of cosmetic deformity, as measured by the popeye deformity. The presented study is an evidence level 3 trial based on 83 patients and contributes to the need for high-level evidence on this topic. Unfortunately, no sample size calculation was performed prior to the initiation of this study. Because the highest level of evidence is a meta-analysis, we conducted a literature search in Pubmed/Medline with the search terms biceps tendon, tenotomy, tenodesis, rotator cuff, and shoulder. Based on this search, we found 4 similar studies that provided data on Constant score or popeye signs, which enabled us to conduct a meta-analysis on the effectiveness of tenotomy versus tenodesis of the long head of the biceps when performed with rotator cuff repair, and we found that 372 patients could be added to the 83 patients in Cho et al study, which is the most recent trial published in this journal. The results of our meta-analysis showed a higher incidence of the popeye sign in the patients with a tenotomy compared with patients with a tenodesis of the long head of the biceps (Figure 1). In previous studies there seemed to be no difference in clinical outcome assessed by the Constant score. Our meta-analysis revealed a strong trend to a difference in functional outcome (Figure 2) in favor of the tenodesis patients. However, a significant difference was not established (95% CI, 0.09-5.68). The Constant score was also assessed with the fixed-effects model, and this did not show different results. The Constant score is not specifically designed or validated to measure functional performance of the shoulder after long head biceps treatment. It is difficult to isolate the influence of the biceps treatment on the functional outcome when performed in combination with a cuff repair. The lack of a statistically significant difference in clinical outcome may therefore not be a correct reflection of the patients’ perceived functional results of biceps treatment. Pooling the data from different trials can help in this respect. Updating meta-analyses on a regular basis provides the physician with up-to-date best evidence and helps them in decision making in clinical practice. Currently, 3 new trials are recruiting patients, and an update of our meta-analysis should be performed after these highquality trials, reporting on patient-related outcome measures such as complication rate and validated patient-reported outcomes, are finished.
Radial Artery Thrombosis in a Young Athlete

Occlusive vascular disease in the upper extremity of athletes is rare and is usually caused by repeated or isolated blunt trauma. The artery most commonly involved is the ulnar artery where it emerges from the canal of Guyon and runs across the superficial hypothenar musculature. We report an isolated radial artery thrombosis, documented with arteriography, caused by a single athletic injury. To our knowledge, posttraumatic thrombosis of the radial artery in the anatomic snuff box associated with distal embolic disease has not been reported. Treatment options are discussed.
A new function of microtubule-associated protein tau: Involvement in chromosome stability

Tau is a microtubule-associated protein that promotes assembly and stabilization of cytoskeleton microtubules. It is mostly expressed in neuronal and glial cells but it is also present in non-neural cells such as fibroblasts and lymphocytes. An altered tau produces cytoskeleton pathology resulting in neurodegenerative diseases such as Alzheimer’s disease and tauopathies. Tau has been suggested to be a multifunctional protein, due to its localization in different cellular compartments. However its further functions are still unclear. We analyzed the distribution of tau in human skin fibroblasts showing its localization in the nucleus and along mitotic chromosomes. Then, we investigated if an altered tau, such as the P301L mutated protein associated with frontotemporal dementia, could produce nuclear pathology. We found that patients carrying the mutation consistently had several chromosome aberrations in their fibroblasts and lymphocytes: chromosome and chromatid breakages or gaps, aneuploidies, translocations, in addition to chromatin bridges and decondensed chromosomes. Our findings argue for a role of tau in chromosome stability by means of its interaction with both microtubules and chromatin.
Assessment of shoulder strength in professional baseball pitchers.

STUDY DESIGN A bilateral comparison of strength and range of motion testing in professional baseball pitchers. OBJECTIVE We studied 39 professional male baseball pitchers to determine if the shoulder used for throwing was weaker or had less passive range of motion, compared to the nondominant arm. BACKGROUND Shoulder muscle weakness has been proposed as a possible risk factor for developing injury. Therefore, objective quantification of the strength of glenohumeral and scapular rotator muscle groups should be studied in a population of professional baseball pitchers. METHODS AND MEASURES Passive internal and external range of motion was bilaterally measured at 90 degrees of abduction. Muscle strength of the following muscles was measured bilaterally with a hand-held dynamometer: external and internal glenohumeral rotators, supraspinatus, middle trapezius, lower trapezius, and serratus anterior. RESULTS Passive external rotation of the glenohumeral joint at 90 degrees of abduction on the pitching side was significantly greater than on the nonpitching side. Passive internal rotation range of motion on the nonpitching side was significantly greater than on the pitching side. The pitching arm's internal rotators, when tested in abduction, were significantly stronger than the nonpitching arm. The nonpitching arm's external rotators in the plane of the scapula, and in abduction, were significantly greater than those of the pitching arm. The pitching arm's middle and lower trapezius muscles were significantly stronger than those of the nonpitching arm. CONCLUSION The range of motion and strength characteristics measured in this study can assist clinicians in evaluating athletes who use overhead throwing motions.