Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete mitochondrial genome of the Korean ikonnikov’s bat Myotis ikonnikovi (Chiroptera: Vespertilionidae)

Abstract We have characterized the complete mitochondrial genome of a Korean ikonnikov’s bat species, Myotis ikonnikovi. Total length of the mitogenome is 16,585 bp with a total base composition of 34.0% A, 30.4% T, 22.8% C and 12.8% G. The mitogenome consists of 13 protein-coding genes, 2 rRNA (12S and 16S RNA) genes, 22 tRNA genes and 1 control region. The mitogenome of M. ikonnikovi exhibited similar features compared with the previously determined mitogenome of a Myotis species, M. formosus. The results will contribute to our understanding of the mechanisms underlying mitogenome evolution in the genus Myotis bats.
Semi-Supervised Discriminant Analysis using robust path-based similarity

Linear discriminant analysis (LDA), which works by maximizing the within-class similarity and minimizing the between-class similarity simultaneously, is a popular dimensionality reduction technique in pattern recognition and machine learning. In real-world applications when labeled data are limited, LDA does not work well. Under many situations, however, it is easy to obtain unlabeled data in large quantities. In this paper, we propose a novel dimensionality reduction method, called semi-supervised discriminant analysis (SSDA), which can utilize both labeled and unlabeled data to perform dimensionality reduction in the semi-supervised setting. Our method uses a robust path-based similarity measure to capture the manifold structure of the data and then uses the obtained similarity to maximize the separability between different classes. A kernel extension of the proposed method for nonlinear dimensionality reduction in the semi-supervised setting is also presented. Experiments on face recognition demonstrate the effectiveness of the proposed method.
Measurement of catecholamines and their metabolites

Analysis of the low levels of catecholamines and metabolites in tissue and biological fluids has necessitated the use of highly sensitive analytical techniques. Earlier procedures utilizing radioenzymatic and immunological assays, gas chromatography or fluorimetry have generally been superseded by highly sensitive and selective chromatographic methods utilizing electrochemical or fluorimetric detection. The development of high-performance liquid chromatography (HPLC) methods for the measurement of plasma metadrenalines and the combination of HPLC with tandem mass spectrometry provides additional procedures with minimum interference from drugs and drug metabolites. This review summarizes the methodology currently available for the measurement of catecholamines and metabolites in plasma and urine, the influence of sample collection protocols and the clinical application of the methods for the biochemical detection of catecholamine-secreting tumours.
Elevated Plasma Lipoprotein(a) Levels and Hypoalbuminemia in Peritoneal Dialysis Patients

Plasma lipoprotein(a), Lp(a), is strongly and independently associated with atherosclerosis, and levels are elevated in hemodialysis (HD) patients and in some studies of those on peritoneal dialysis (PD). We hypothesized that protein losses and hypoalbuminemia could stimulate hepatic Lp(a) synthesis, and this effect would be accentuated in PD patients with malnutrition. The PD subjects (n=24) had higher plasma Lp(a) levels than those (n=10) on HD (median 34.4 vs 21.0 mg/dl, p<0.05), and values exceed normal in 62.5% vs 20% of the subjects (p<0.03), respectively. The serum albumin levels inversely correlated with concentrations of Lp(a) and apolipoprotein B, as well as the apolipoprotein B/AI ratio. In conclusion, plasma Lp(a) concentrations are frequently elevated in PD as well as HD patients. Measuring Lp(a) levels is useful in identifying patients at increased atherogenic risk, which may not be reflected in routine lipid profiles. The negative correlation between plasma Lp(a) and albumin levels suggests that the latter may be linked pathophysiologically to hepatic Lp(a) production. The association of hypoalbuminemia with higher Lp(a) values is of particular concern because malnutrition frequently occurs in PD patients.
Pharmaceutical Powder Compaction Technology

Interparticulate Bonding Characteristics of Pharmaceutical Compacts Interparticulate Attraction Mechanisms, Claus Fuhrer The Importance of Intermolecular Bonding Forces and the Concept of Bonding Surface Area, Christer Nystrom and Per-Gunnar Karehill Characterization of the Compression Process Porosity-Pressure Functions, Petteri Paronen and Jukka Ilkka Force-Displacement and Network Measurements, Gert Ragnarsson Viscoelastic Models, Fritz Muller Application of Percolation Theory and Fractal Geometry to Tablet Compaction, Hans Leuenberger, Ruth Leu, and Jean-Daniel Bonny Characterization of Compact Properties Mechanical Strength, Peter N. Davies and J. Michael Newton Tablet Surface Area, N. Anthony Armstrong Rationale for and the Measurement of Tableting Indices, Everett N. Hiestand Material Properties of Importance for Powder Volume Reduction and Compact Strength Particle Dimensions, Goran Alderborn Mechanical Properties, Ray C. Rowe and Ron J. Roberts Granule Properties, Goran Alderborn and Martin Wikberg Modeling the Compression Behavior of Particle Assemblies from the Mechanical Properties of Individual Particles, Wendy C. Duncan-Hewitt Compaction Properties of Excipients and Powder Mixtures Materials for Direct Compaction, Gerald K. Bolhuis and Zak T. Chowhan Compaction Properties of Binary Mixtures, John T. Fell Lubricant Sensitivity, Gerad K. Bolhuis and Arne W. Holzer The Development and Optimization of Tablet Formulations Using Mathematical Methods, Fridrun Podczeck
Diagnosis, Clinical Features, and Self-Reported Morbidity of Strongyloides stercoralis and Hookworm Infection in a Co-Endemic Setting

Background Infections with Strongyloides stercoralis and other helminths represent important, yet often neglected issues in developing countries. Indeed, strongyloidiasis can be fatal, but only a few studies provide information regarding its health relevance in Africa. Moreover, clinical data on symptomatology and typical recognition patterns mainly originate from Western travel clinics. Methodology A cross-sectional epidemiological survey was carried out in a rural part of south-central Côte d'Ivoire. Stool samples from 292 randomly selected individuals were examined for intestinal helminths, using a suite of diagnostic techniques (i.e., Kato-Katz, Baermann funnel, and Koga agar plate). Participants were interviewed with a pre-tested questionnaire and clinically examined. Multivariate logistic regression analysis was done to relate perceived morbidity and clinical findings to helminth infection status. Principal Findings The prevalence of hookworm and S. stercoralis was 51.0% and 12.7%, respectively. Both infections were strongly associated with each other (adjusted odds ratio, 6.73; P<0.001) and higher prevalences were observed with age. S. stercoralis-infected individuals expressed self-reported morbidity considerably more often than those with hookworm infection. Clinical examination identified high prevalences of various pathologies and detected tendencies to worse health conditions in helminth-infected subjects. Conclusions/Significance The use of multiple diagnostic tools showed that S. stercoralis and hookworm are co-endemic in rural Côte d'Ivoire and that each infection causes clinical symptoms and sequelae. Our findings are important for (re-)estimating the burden of helminth infections, and highlight the need for integrating epidemiological surveys, rigorous diagnostic approaches, and clinical assessments in the developing world.
Statistical Features of Short-Period and Long-Period Near-Source Ground Motions

Abstract This study collects recorded ground motions from the near-source region of large earthquakes and considers to what extent this historic record can inform expectations of future ground motions at similar sites. The distribution of observed peak ground acceleration (PGA) is well approximated by the lognormal distribution, and we expect the observed distribution to remain unchanged with the addition of data from future earthquakes. However, the distribution of peak ground displacements (PGD) will likely change after a well-recorded large earthquake. Specifically we expect future observations of PGD greater than those previously recorded. We use seismic scaling relations to motivate the expected distribution of PGD as uniform on the logarithmic scale, or at least fat-tailed. Because PGA does not scale with fault rupture area or slip on the fault, there are no such scaling relations to predict the observed distribution of PGA. The observed records show that there is essentially no correlation between PGD and PGA for near-source ground motions from large events. The large uncertainty in a future value of PGD in the near-source region of a large earthquake exists despite the ability of Earth scientists to accurately model long-period ground motions. In contrast, the relative certainty in a future value of PGA exists despite the inability to model short-period ground motions reliably. The stability of the observed distribution of PGA with respect to new ground-motion records enables us to predict the distribution of future PGA and to calculate the probability of exceeding the largest recorded PGA.
Bita: Coverage-guided, automatic testing of actor programs

Actor programs are concurrent programs where concurrent entities communicate asynchronously by exchanging messages. Testing actor programs is challenging because the order of message receives depends on the non-deterministic scheduler and because exploring all schedules does not scale to large programs. This paper presents Bita, a scalable, automatic approach for testing non-deterministic behavior of actor programs. The key idea is to generate and explore schedules that are likely to reveal concurrency bugs because these schedules increase the schedule coverage. We present three schedule coverage criteria for actor programs, an algorithm to generate feasible schedules that increase coverage, and a technique to force a program to comply with a schedule. Applying Bita to real-world actor programs implemented in Scala reveals eight previously unknown concurrency bugs, of which six have already been fixed by the developers. Furthermore, we show our approach to find bugs 122× faster than random scheduling, on average.
Anaphylaxis with clonal mast cells in normal looking skin – a new entity?

Patients with elevated basal tryptase (sBT) >15 μg/l and anaphylaxis may have an underlying mastocytosis. A monoclonal mast cell activation syndrome with aberrant mast cells (MC) at extracutaneous sites has been described in patients with severe hypotension or anaphylaxis.
Hankel singular value functions from Schmidt pairs for nonlinear input-output systems

In this paper three results are presented in singular value analysis of Hankel operators for nonlinear input-output systems. First the notion of a Schmidt pair is introduced which makes it possible to describe a Hankel singular value function from a purely input-output point of view. If a state space realization is known to exist then a set of sufficient conditions is provided for the existence of a Schmidt pair. Finally, it is shown that in a certain coordinate frame it is possible to relate this new singular value function definition to the existing definition due to Scherpen (1993, 1995).
Efficient partial-duplicate detection based on sequence matching

With the ever-increasing growth of the Internet, numerous copies of documents become serious problem for search engine, opinion mining and many other web applications. Since partial-duplicates only contain a small piece of text taken from other sources and most existing near-duplicate detection approaches focus on document level, partial duplicates can not be dealt with well. In this paper, we propose a novel algorithm to realize the partial-duplicate detection task. Besides the similarities between documents, our proposed algorithm can simultaneously locate the duplicated parts. The main idea is to divide the partial-duplicate detection task into two subtasks: sentence level near-duplicate detection and sequence matching. For evaluation, we compare the proposed method with other approaches on both English and Chinese web collections. Experimental results appear to support that our proposed method is effectively and efficiently to detect both partial-duplicates on large web collections.
Ki-67: a useful marker for the evaluation of dysplasia in ulcerative colitis.

AIMS: Evaluation of dysplasia in long standing ulcerative colitis is a difficult and often subjective task. Therefore, the aim of this study was to search for a more objective parameter to help distinguish regenerative changes from epithelial dysplasia. METHODS: A total of 97 sections from colectomy specimens from 12 patients with ulcerative colitis of more than 10 years duration were stained immunohistochemically with MIB 1 to detect differences in the frequency and pattern of nuclei positive for the proliferation marker Ki-67. All patients had epithelial dysplasia in one or more areas (high grade dysplasia, n = 16; low grade dysplasia, n = 15; indefinite for dysplasia, n = 16), and three patients had additional adenocarcinoma (one Dukes's C multifocal, mucinous carcinoma; one Dukes's C adenocarcinoma in the sigmoid; and one Dukes's A adenocarcinoma in the caecum). Two patients had adenomas--one had an 8 cm villous adenoma with intramucosal carcinoma, and the other had a 4 cm tubulovillous adenoma with high grade dysplasia. RESULTS: There were highly significant differences between the percentages of Ki-67 immunopositive cells in low grade and high grade dysplasia and carcinoma compared with regenerative epithelium. In high grade dysplasia and carcinoma, the distribution of Ki-67 positive cells was diffuse throughout the full length of the crypt, whereas low grade dysplasia and epithelium indefinite for dysplasia, as well as regenerative epithelium, showed an expanded basal zone. CONCLUSIONS: Assessment of the number of Ki-67 immunostained cells is of additional value in deciding whether the mucosa is regenerative or dysplastic, and the MIB 1 staining pattern is characteristic for most lesions with high grade dysplasia and carcinoma. Therefore, this technique could be combined with routine histological evaluation of colorectal epithelium being examined for dysplasia.
What HeLa Cells Are You Using

The HeLa cell line, named after the patient Henrietta Lacks, was one the first human cell lines to be used for tissue culture. In the decades since its origin, it has become a feature in labs across the world. Despite its longevity, repeated detection of most HeLa marker chromosomes have lead the scientific community to view HeLa as a stable cell line and its corresponding findings to be reproducible. However, to date no investigation has examined other meaningful aspects of HeLa's genomic variability, such has whether HeLa's modal chromosome number remains constant. Considering the importance of a cell line's karyotype with respect to reproducibility, I sought to examine the stability of HeLa's karyotype by examining HeLa's modal chromosome number as reported in the literature. 1
Metabolomics in Angiotensin II–Induced Cardiac Hypertrophy

Angiotensin II (Ang II) induces mitochondrial dysfunction. We tested whether Ang II alters the “metabolomic” profile. We harvested hearts from 8-week–old double transgenic rats harboring human renin and angiotensinogen genes (dTGRs) and controls (Sprague-Dawley), all with or without Ang II type 1 receptor (valsartan) blockade. We used gas chromatography coupled with time-of-flight mass spectrometry to detect 247 intermediary metabolites. We used a partial least-squares discriminate analysis and identified 112 metabolites that differed significantly after corrections (false discovery rate q <0.05). We found great differences in the use of fatty acids as an energy source, namely, decreased levels of octanoic, oleic, and linoleic acids in dTGR (all P<0.01). The increase in cardiac hypoxanthine levels in dTGRs suggested an increase in purine degradation, whereas other changes supported an increased ketogenic amino acid tyrosine level, causing energy production failure. The metabolomic profile of valsartan-treated dTGRs more closely resembled Sprague-Dawley rats than untreated dTGRs. Mitochondrial respiratory chain activity of cytochrome C oxidase was decreased in dTGRs, whereas complex I and complex II were unaltered. Mitochondria from dTGR hearts showed morphological alterations suggesting increased mitochondrial fusion. Cardiac expression of the redox-sensitive and the cardioprotective metabolic sensor sirtuin 1 was increased in dTGRs. Interestingly, valsartan changed the level of 33 metabolites and induced mitochondrial biogenesis in Sprague-Dawley rats. Thus, distinct patterns of cardiac substrate use in Ang II–induced cardiac hypertrophy are associated with mitochondrial dysfunction. The finding underscores the importance of Ang II in the regulation of mitochondrial biogenesis and cardiac metabolomics, even in healthy hearts.
Frontiers in Integrative Neuroscience Integrative Neuroscience Neural Synchrony in Cortical Networks: History, Concept and Current Status

Following the discovery of context-dependent synchronization of oscillatory neuronal responses in the visual system, the role of neural synchrony in cortical networks has been expanded to provide a general mechanism for the coordination of distributed neural activity patterns. In the current paper, we present an update of the status of this hypothesis through summarizing recent results from our laboratory that suggest important new insights regarding the mechanisms, function and relevance of this phenomenon. In the fi rst part, we present recent results derived from animal experiments and mathematical simulations that provide novel explanations and mechanisms for zero and nero-zero phase lag synchronization. In the second part, we shall discuss the role of neural synchrony for expectancy during perceptual organization and its role in conscious experience. This will be followed by evidence that indicates that in addition to supporting conscious cognition, neural synchrony is abnormal in major brain disorders, such as schizophrenia and autism spectrum disorders. We conclude this paper with suggestions for further research as well as with critical issues that need to be addressed in future studies. comprise phenomena such as self-generated network oscillations, synchronization and phase locking. An important link between temporal patterning of neuronal activity and cortical computations was the discovery that oscillatory rhythms in the beta/gamma range (20–80 Hz) serve to establish precise and context dependent temporal relations – in this case synchrony – between distributed neural discharges. Gray et al. (1989) showed that action potentials generated by cortical cells align with the oscillatory rhythm which has the consequence that neurons phase locked to synchronized oscillations, synchronize their discharges with high precision. More recent evidence indicates that these oscillations are not only instrumental for the synchronization of neuronal discharges but can support also other consistent temporal relations by establishing systematic phase lags between the discharges of distributed neurons. In-vitro studies (Volgushev et al., 1998) and multi-site recordings in the visual cortex of cats (Fries et al., 2001b) provided evidence, that the oscillatory pat-terning of neuronal activity is an effi cient mechanism to adjust the precise timing of spikes and is potentially a versatile mechanism to convert rate coded input to cells into a temporal code defi ned by the time of occurrence of spikes relative to the oscillation cycle (see also Fries et al., 2007). Following the initial descriptions of context dependent synchronization in the visual cortex, numerous studies have been initiated in order to investigate …
An Introduction to Monte Carlo Simulation of Statistical physics Problem

A brief introduction to the technique of Monte Carlo for simulation of statistical physics problems is presented. Ising spin model is taken as an example. The topics covered include random and pseudo random numbers, random sampling techniques, Markov chain, Metropolis algorithm, continuous phase transition, statistical errors from correlated and uncorrelated data, nite size scaling, critical slowing down , cluster algorithms,
Human duodenal phase III migrating motor complex activity is predominantly antegrade, as revealed by high‐resolution manometry and colour pressure plots

Abstract Late phase III migrating motor complex activity has been said to be primarily retroperistaltic but has not been assessed with high resolution manometry or three‐dimensional colour pressure plots (pressure/time/distance). Duodenal phase III was examined in healthy young volunteers (seven male, two female) with a 20‐lumen assembly. With the most proximal sidehole in the distal antrum, after a 4.5‐cm interval 18 sideholes at 1.5‐cm intervals spanned the duodenum with a final sidehole 3 cm beyond. Fasting pressures were recorded until phase III occurred. Comparisons were made between proximal (P) and distal (D) duodenum during early (E) (first 0.5–1 min) and late (L) (last 0.5–1 min) phase III. With colour pressure analysis, 121 of 180 pressure wave (PW) sequences were purely antegrade, two purely retrograde and 57 bidirectional. Ten of fifty‐seven bidirectional PW sequences were complex, branching to become two separate sequences. Bidirectional sequences occurred more frequently in late than early phase III (L 43 vs. E 14 of 57), but their occurrence did not differ between proximal and distal duodenum (P31 vs. D 24 of 57). Antegrade propagation velocity was faster in late compared with early phase III (L 28.50 vs. E 17.05 mm s−1; P = 0.006), but did not differ between proximal and distal duodenum. Colour pressure analysis also indicated an intermittent segmental pattern to phase III, with each subject exhibiting a change in velocity or direction, or a relative failure of peristalsis somewhere along the duodenum during part of phase III. Duodenal phase III is not homogenous and, in contrast with previous studies, does not primarily constitute a retroperistaltic pump. Colour pressure analysis is useful in interpreting intraluminal pressure profiles and may improve the sensitivity and specificity of clinical studies.
A Family of Tractable Graph Distances

Important data mining problems such as nearest-neighbor search and clustering admit theoretical guarantees when restricted to objects embedded in a metric space. Graphs are ubiquitous, and clustering and classification over graphs arise in diverse areas, including, e.g., image processing and social networks. Unfortunately, popular distance scores used in these applications, that scale over large graphs, are not metrics and thus come with no guarantees. Classic graph distances such as, e.g., the chemical and the CKS distance are arguably natural and intuitive, and are indeed also metrics, but they are intractable: as such, their computation does not scale to large graphs. We define a broad family of graph distances, that includes both the chemical and the CKS distance, and prove that these are all metrics. Crucially, we show that our family includes metrics that are tractable. Moreover, we extend these distances by incorporating auxiliary node attributes, which is important in practice, while maintaining both the metric property and tractability.