Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota)

Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.
Lack of Association Between Epicardial Fat Volume and Extent of Coronary Artery Calcification, Severity of Coronary Artery Disease, or Presence of Myocardial Perfusion Abnormalities in a Diverse, Symptomatic Patient Population: Results From the CORE320 Multicenter Study

Background—Epicardial fat may play a role in the pathogenesis of coronary artery disease (CAD). We explored the relationship of epicardial fat volume (EFV) with the presence and severity of CAD or myocardial perfusion abnormalities in a diverse, symptomatic patient population. Methods and Results—Patients (n=380) with known or suspected CAD who underwent 320-detector row computed tomographic angiography, nuclear stress perfusion imaging, and clinically driven invasive coronary angiography for the CORE320 international study were included. EFV was defined as adipose tissue within the pericardial borders as assessed by computed tomography using semiautomatic software. We used linear and logistic regression models to assess the relationship of EFV with coronary calcium score, stenosis severity by quantitative coronary angiography, and myocardial perfusion abnormalities by single photon emission computed tomography (SPECT). Median EFV among patients (median age, 62.6 years) was 102 cm3 (interquartile range: 53). A coronary calcium score of ≥1 was present in 83% of patients. Fifty-nine percent of patients had ≥1 coronary artery stenosis of ≥50% by quantitative coronary angiography, and 49% had abnormal myocardial perfusion results by SPECT. There were no significant associations between EFV and coronary artery calcium scanning, presence severity of ≥50% stenosis by quantitative coronary angiography, or abnormal myocardial perfusion by SPECT. Conclusions—In a diverse population of symptomatic patients referred for invasive coronary angiography, we did not find associations of EFV with the presence and severity of CAD or with myocardial perfusion abnormalities. The clinical significance of quantifying EFV remains uncertain but may relate to the pathophysiology of acute coronary events rather than the presence of atherosclerotic disease.
Prevalence and Characterization of Escherichia coli and Salmonella Strains Isolated from Stray Dog and Coyote Feces in a Major Leafy Greens Production Region at the United States-Mexico Border

In 2010, Romaine lettuce grown in southern Arizona was implicated in a multi-state outbreak of Escherichia coli O145:H28 infections. This was the first known Shiga toxin-producing E. coli (STEC) outbreak traced to the southwest desert leafy green vegetable production region along the United States-Mexico border. Limited information exists on sources of STEC and other enteric zoonotic pathogens in domestic and wild animals in this region. According to local vegetable growers, unleashed or stray domestic dogs and free-roaming coyotes are a significant problem due to intrusions into their crop fields. During the 2010–2011 leafy greens growing season, we conducted a prevalence survey of STEC and Salmonella presence in stray dog and coyote feces. Fresh fecal samples from impounded dogs and coyotes from lands near produce fields were collected and cultured using extended enrichment and serogroup-specific immunomagnetic separation (IMS) followed by serotyping, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing. A total of 461 fecal samples were analyzed including 358 domestic dog and 103 coyote fecals. STEC was not detected, but atypical enteropathogenic E. coli (aEPEC) strains comprising 14 different serotypes were isolated from 13 (3.6%) dog and 5 (4.9%) coyote samples. Salmonella was cultured from 33 (9.2%) dog and 33 (32%) coyote samples comprising 29 serovars with 58% from dogs belonging to Senftenberg or Typhimurium. PFGE analysis revealed 17 aEPEC and 27 Salmonella distinct pulsotypes. Four (22.2%) of 18 aEPEC and 4 (6.1%) of 66 Salmonella isolates were resistant to two or more antibiotic classes. Our findings suggest that stray dogs and coyotes in the desert southwest may not be significant sources of STEC, but are potential reservoirs of other pathogenic E. coli and Salmonella. These results underscore the importance of good agriculture practices relating to mitigation of microbial risks from animal fecal deposits in the produce production area.
Studies on characterization, standardization of technology and shelf-life of cham-cham.

Cham-cham is an indigenous, chhana-based sweetmeat popular in eastern part of India. It is produced from cow milk chhana. Promising development and expansion in the market of chamcham is expected in the coming future with the organized production of this product at commercial scale. This project was undertaken with the major objective of standardized technology development for cham-cham production. The extent of variation in physicochemical, textural and sensory properties of market samples of cham-cham was estimated and the attributes that govern much of variation in sensory scores of this product were identified using quantitative descriptive analysis and principal component analysis. In the production of cham-cham, slight variations in the processing parameters such as powdered sugar (PS) addition, cooking syrup concentration (CSC), cooking time (CT) and soaking syrup concentration (SSC) can affect the quality significantly. Hence, the processing parameters were standardized using response surface methodology (RSM) and their effect on texture, microstructure, physicochemical and sensory attributes of cham-cham were studied. The solution having maximum desirability of 0.824, corresponding to 5% PS, 80 °Brix CSC, 30 min CT and 60 °Brix SSC, was selected as optimized condition for cham-cham preparation. Scanning electron microscopy study effectively described the changes occurred in protein and fat phase of cham-cham during cooking. Moisture sorption study of cham-cham was carried out at three temperatures i.e. 5°C, 25°C, and 40°C to obtain sorption isotherms. BET, Modified Mizrahi and Henderson model gave best fit. Density of sorbed water, number of adsorbed monolayers, per cent bound water, surface area of adsorbent and porosity were calculated. The net isosteric heat and enthalpy–entropy compensation theory was also measured. Shelf life study of cham-cham was performed in cardboard box, polyethylene/nylon pouch for vacuum packaging, 12μ polyethylene teraphthalate (PET) /12μ metalized polyethylene teraphthalate (MPET) /50μ low density polyethylene (LDPE) laminate pouches and tin cans. Physico-chemical, textural, sensory and microbial changes were estimated. At 30oC, shelf life of cham-cham was 7 days in all three packaging materials. At 5oC, cham-cham was acceptable upto 14, 21 and 35 days in cardboard box, vacuum packaging and laminate pouch, respectively. In cans, cham-cham was found acceptable against physicochemical and microbial changes upto 35 days. In consumer study it was found that maximum consumer (50%) rated as “very good”, 25% consumers rated “good” and 17% rated “excellent” degree of liking. About 86% of the consumers were ready to buy the cham-cham even at the prices higher than that of market.
Tree diversity of the Dja Faunal Reserve, southeastern Cameroon

Abstract The Dja Faunal Reserve located in southeastern Cameroon represents the largest and best protected rainforest patch in Cameroon. Here we make available a dataset on the inventory of tree species collected across the Dja. For this study nine 5 km long and 5 m wide transects were installed. All species with a diameter at breast height greater than 10 cm were recorded, identified and measured. A total of 11546 individuals were recorded, corresponding to a total of 312 species identified with 60 genera containing unidentified taxa. Of the 54 identified families Fabaceae, Rubiaceae and Malvaceae were the most species rich, whereas Fabaceae, Phyllantaceae and Olacaceae were the most abundant. Finally, Tabernaemontana crassa was the most abundant species across the Reserve. This dataset provides a unique insight into the tree diversity of the Dja Faunal Reserve and is now publically available and usable.
Secure Spread Image Watermarking Scheme in 3D-DCT Domain

In this paper, a robust secure spread based image watermarking scheme based on 3-dimensional discrete cosine transform(3D-DCT) is proposed for copyright protection. Firstly, the color image is divided into 3-D blocks, and then these blocks are transformed into transform domain by 3D DCT transform, finally, the generated pseudo random sequence, as the watermark embedded, is embedded into the selected coefficients. Since the pixels among different color channels is much relative, the watermark can be embedded with good robustness in secure spread manner. The theoretic analysis and the experimental results support the conclusion well. KeywordsWatermarking, 3-D DCT, Robust, color image
Effects of Substitution of Fish Meal with Black Soldier Fly (Hermetia illucens) Larvae Meal, in Yellow Catfish (Pelteobagrus fulvidraco) Diets

An 8-week feeding trial was conducted to evaluate effects of replacing fish meal (FM) with black soldier fly larvae meal (BSF) on growth performance, feed utilization, and plasma parameters, for juvenile yellow catfish, Pelteobagrus fulvidraco. Six isonitrogenous and isolipidic diets were prepared substituting the FM protein with BSF protein in the following amounts: 0 (control group), 10% (BSF10), 15% (BSF15), 20% (BSF20), 25% (BSF25) and 30% (BSF30). Three replicate groups of juvenile yellow catfish (initial weight of 1.20 ± 0.01 g) were stocked in circular tanks at a rate of 30 fish per tank. The results showed that 20% of the FM in the control diet could be replaced with BSF without significantly reducing weight gain, feed conversion ratio, or whole body and muscle proximate composition. Apparent digestibility coefficients (ADCs) of dry matter, crude protein, crude lipids, gross energy, or amino acids were not affected by 10% FM replacement. 30% FM replacement in the BSF30 diet significantly increased the concentration of cholesterol (CHO) and nitric oxide (NO) in the plasma, and significantly reduced the inhibition of superoxide radical anion formation. In conclusion, it appears that up to 20% of the FM in conventional yellow catfish diets can be replaced with BSF, and thus account for up to 8.9% of the total protein in the diet without causing a significant reduction in growth performance. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.
Body-Shape Transfer for Super Deformation of 3D Character Models

We present a technique for semi-automatically super-deforming 3D character models. Super deformation is a unique style of exaggeration, often seen in Japanese animation and manga, to enhance characters' cute appearances. Specifically, super-deformed (SD) characters are chubby with stubby limbs and oversized heads. Given a reference SD model with a rig and a target character model, our method automatically calculates a rig of the target model, measures the body shapes, and shortens the target limbs and enlarges the target head by transferring the reference body shape. Our method further makes the target face younger by applying a simple deformation based on a biological insight. We demonstrate that our method can create visually-pleasing SD character models quickly.
The Human Skeletal Muscle Na Channel Mutation R669H Associated with Hypokalemic Periodic Paralysis Enhances Slow Inactivation

Missense mutations of the human skeletal muscle voltage-gated Na channel (hSkM1) underlie a variety of diseases, including hyperkalemic periodic paralysis (HyperPP), paramyotonia congenita, and potassium-aggravated myotonia. Another disorder of sarcolemmal excitability, hypokalemic periodic paralysis (HypoPP), which is usually caused by missense mutations of the S4 voltage sensors of the L-type Ca channel, was associated recently in one family with a mutation in the outermost arginine of the IIS4 voltage sensor (R669H) of hSkM1 (Bulman et al., 1999). Intriguingly, an arginine-to-histidine mutation at the homologous position in the L-type Ca2+ channel (R528H) is a common cause of HypoPP. We have studied the gating properties of the hSkM1-R669H mutant Na channel experimentally in human embryonic kidney cells and found that it has no significant effects on activation or fast inactivation but does cause an enhancement of slow inactivation. R669H channels exhibit an ∼10 mV hyperpolarized shift in the voltage dependence of slow inactivation and a twofold to fivefold prolongation of recovery after prolonged depolarization. In contrast, slow inactivation is often disrupted in HyperPP-associated Na channel mutants. These results demonstrate that, in R669H-associated HypoPP, enhanced slow inactivation does not preclude, and may contribute to, prolonged attacks of weakness and add support to previous evidence implicating the IIS4 voltage sensor in slow-inactivation gating.
Analysis of DCTCP: stability, convergence, and fairness

Cloud computing, social networking and information networks (for search, news feeds, etc) are driving interest in the deployment of large data centers. TCP is the dominant Layer 3 transport protocol in these networks. However, the operating conditions---very high bandwidth links, low round-trip times, small-buffered switches---and traffic patterns cause TCP to perform very poorly. The Data Center TCP (DCTCP) algorithm has recently been proposed as a TCP variant for data centers and addresses these shortcomings. In this paper, we provide a mathematical analysis of DCTCP. We develop a fluid model of DCTCP and use it to analyze the throughput and delay performance of the algorithm, as a function of the design parameters and of network conditions like link speeds, round-trip times and the number of active flows. Unlike fluid model representations of standard congestion control loops, the DCTCP fluid model exhibits limit cycle behavior. Therefore, it is not amenable to analysis by linearization around a fixed point and we undertake a direct analysis of the limit cycles, proving their stability. Using a hybrid (continuous- and discrete-time) model, we analyze the convergence of DCTCP sources to their fair share, obtaining an explicit characterization of the convergence rate. Finally, we investigate the "RTT-fairness" of DCTCP; i.e., the rate obtained by DCTCP sources as a function of their RTTs. We find a very simple change to DCTCP which is suggested by the fluid model and which significantly improves DCTCP's RTT-fairness. We corroborate our results with ns2 simulations.
Automatic punctuation and disfluency detection in multi-party meetings using prosodic and lexical cues

We investigate automatic approaches to ﬁnding “hidden” sponta-neous speech events, such as sentence boundaries and disﬂuencies, in multi-party meetings. Hidden events are characterized prosod-ically by a large array of automatically extracted energy, duration, and pitch features, and are modeled by decision tree classi-ﬁers; lexical cues are modeled by N-gram language models. Both sources of information are combined in a hidden Markov model framework. Results show that combined classiﬁers achieve higher accuracy than either single knowledge source alone. We also study classiﬁers that use only the preceding context for predicting events, simulating online processing. We ﬁnd that prosodic features are more robust than are language model features to this constraint. Finally, we examine the effect of automatic word recognition errors, in both training and testing, on classiﬁcation accuracy. We ﬁnd that lexical models degrade much more severely than do prosodic models in this case, again showing the relative robustness of prosodic information for hidden-event detection in natural conversation.
European Society of Gynaecologic Oncology Quality Indicators for Advanced Ovarian Cancer Surgery

Objectives The surgical management of advanced ovarian cancer involves complex surgery. Implementation of a quality management program has a major impact on survival. The goal of this work was to develop a list of quality indicators (QIs) for advanced ovarian cancer surgery that can be used to audit and improve the clinical practice. This task has been carried out under the auspices of the European Society of Gynaecologic Oncology (ESGO). Methods Quality indicators were based on scientific evidence and/or expert consensus. A 4-step evaluation process included a systematic literature search for the identification of potential QIs and the documentation of scientific evidence, physical meetings of an ad hoc multidisciplinarity International Development Group, an internal validation of the targets and scoring system, and an external review process involving physicians and patients. Results Ten structural, process, or outcome indicators were selected. Quality indicators 1 to 3 are related to achievement of complete cytoreduction, caseload in the center, training, and experience of the surgeon. Quality indicators 4 to 6 are related to the overall management, including active participation to clinical research, decision-making process within a structured multidisciplinary team, and preoperative workup. Quality indicator 7 addresses the high value of adequate perioperative management. Quality indicators 8 to 10 highlight the need of recording pertinent information relevant to improvement of quality. An ESGO-approved template for the operative report has been designed. Quality indicators were described using a structured format specifying what the indicator is measuring, measurability specifications, and targets. Each QI was associated with a score, and an assessment form was built. Conclusions The ESGO quality criteria can be used for self-assessment, for institutional or governmental quality assurance programs, and for the certification of centers. Quality indicators and corresponding targets give practitioners and health administrators a quantitative basis for improving care and organizational processes in the surgical management of advanced ovarian cancer.
Comparison of treatment effects between the modified C-palatal plate and cervical pull headgear for total arch distalization in adults

Objective The purpose of this study was to evaluate the dental and skeletal effects of the modified C-palatal plate (MCPP) for total arch distalization in adult patients with Class II malocclusion and compare the findings with those of cervical pull headgear. Methods The study sample consisted of the lateral cephalograms of 44 adult patients with Class II Division 1 malocclusion, including 22 who received treatment with MCPP (age, 24.7 ± 7.7 years) and 22 who received treatment with cervical pull headgear (age, 23.0 ± 7.7 years). Pre- (T1) and post-treatment (T2) cephalograms were analyzed for 24 linear and angular measurements. Multivariate analysis of variance was performed to evaluate the changes after treatment in each group and differences in treatment effects between the two groups. Results The mean amount of distalization at the crown and root levels of the maxillary first molar and the amount of distal tipping was 4.2 mm, 3.5 mm, and 3.9° in the MCPP group, and 2.3 mm, 0.6 mm, and 8.6° in the headgear group, respectively. In addition, intrusion by 2.5 mm was observed in the MCPP group. In both groups, the distal movement of the upper lip and the increase in the nasolabial angle were statistically significant (p < 0.001). However, none of the skeletal and soft tissue variables exhibited significant differences between the two groups. Conclusions The results of this study suggest that MCPP is an effective treatment modality for total arch distalization in adults.
A widely applicable Bayesian information criterion

A statistical model or a learning machine is called regular if the map taking a parameter to a probability distribution is one-to-one and if its Fisher information matrix is always positive definite. If otherwise, it is called singular. In regular statistical models, the Bayes free energy, which is defined by the minus logarithm of Bayes marginal likelihood, can be asymptotically approximated by the Schwarz Bayes information criterion (BIC), whereas in singular models such approximation does not hold. Recently, it was proved that the Bayes free energy of a singular model is asymptotically given by a generalized formula using a birational invariant, the real log canonical threshold (RLCT), instead of half the number of parameters in BIC. Theoretical values of RLCTs in several statistical models are now being discovered based on algebraic geometrical methodology. However, it has been difficult to estimate the Bayes free energy using only training samples, because an RLCT depends on an unknown true distribution. In the present paper, we define a widely applicable Bayesian information criterion (WBIC) by the average log likelihood function over the posterior distribution with the inverse temperature 1/log n, where n is the number of training samples. We mathematically prove that WBIC has the same asymptotic expansion as the Bayes free energy, even if a statistical model is singular for or unrealizable by a statistical model. Since WBIC can be numerically calculated without any information about a true distribution, it is a generalized version of BIC onto singular statistical models.