Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of the 2009 (7th Edition) AJCC Melanoma Staging System in the Classification of Thin Cutaneous Melanomas

Context. The 7th (2009) edition of the AJCC melanoma staging system incorporates tumor (Breslow) thickness, MR, and ulceration in stratifying T1 primary melanomas. Compared to the prior 6th (2001) edition, MR has replaced CL for thin melanomas. Objective. We sought to identify and report differences of the classification of thin melanomas as well as outcome of SLNB in patients according to the 6th and 7th editions at our institution. Results. 106 patients were identified with thin melanomas verified by wide excision. 31 of 106 thin melanomas were reclassified according to the 7th edition of the AJCC. Of those 31, 15 CL II/III patients (6th edition T1a) were reclassified as T1b based on the presence of mitoses while 16 CL IV patients (6th edition T1b) were categorized as T1a based on the absence of mitoses. 26/31 reclassified patients underwent SLNB, and all were negative. Patients with thin melanoma and a +SLNB (N = 3) were all classified as T1b according to both staging systems. Conclusions. In our experience, 29% of thin melanomas were reclassified according to the 7th edition with similar proportions of patients re-distributed as T1a (14%) and T1b (15%). Cases with +SLN corresponded with T1b lesions in both 6th and 7th editions.
Spoken word recognition with gender-marked context

In a cross-modal (auditory-visual) fragment priming study in French, we tested the hypothesis that gender information given by a gender-marked article (e.g. unmasculine or unefeminine) is used early in the recognition of the following word to discard gender-incongruent competitors. In four experiments, we compared lexical decision performances on targets primed by phonological information only (e.g. /kRa/-CRAPAUD /kRapo/; /to/-TOAD) or by phonological plus gender information given by a gender-marked article (e.g. unmasculine /kra/-CRAPAUD; a /to/-TOAD). In all experiments, we found a phonological priming effect that was not modulated by the presence of gender context, whether gender-marked articles were congruent (Experiments 1, 2, and 3) or incongruent (Experiment 4) with the target gender. Moreover, phonological facilitation was not modulated by the presence of gender context, whether gender-marked articles allowed exclusion of less frequent competitors (Experiment 1) or more frequent ones (Experiments 2 and 3). We concluded that gender information extracted from a preceding gender-marked determiner is not used early in the process of spoken word recognition and that it may be used in a later selection process.
Fighting fire with fire: using randomized gossip to combat stochastic scalability limits

The mechanisms used to improve the reliability of distributed systems often limit performance and scalability. Focusing on one widely‐used definition of reliability, we explore the origins of this phenomenon and conclude that it reflects a tradeoff arising deep within the typical protocol stack. Specifically, we suggest that protocol designs often disregard the high cost of infrequent events. When a distributed system is scaled, both the frequency and the overall cost of such events often grow with the size of the system. This triggers an O($n^{2}$) phenomenon, which becomes visible above some threshold sizes. Our findings suggest that it would be more effective to construct large‐scale reliable systems where, unlike traditional protocol stacks, lower layers use randomized mechanisms, with probabilistic guarantees, to overcome low‐probability events. Reliability and other end‐to‐end properties are introduced closer to the application. We employ a back‐of‐the‐envelope analysis to quantify this phenomenon for a class of strongly reliable multicast problems. We construct a non‐traditional stack, as described above, that implements virtually synchronous multicast. Experimental results reveal that virtual synchrony over a non‐traditional, probabilistic stack helps break through the scalability barrier faced by traditional implementations of the protocol. Copyright © 2002 John Wiley & Sons, Ltd.
On a problem on explicit embeddings of the group ℚ

Answering a question of de la Harpe and Bridson in the Kourovka Notebook, we build the explicit embeddings of the additive group of rational numbers ℚ in a finitely generated group G. The group G in fact is two-generator, and the constructed embedding can be subnormal and preserve a few properties such as solubility or torsion freeness.
Metal-dependent SpoIIE oligomerization stabilizes FtsZ during asymmetric division in Bacillus subtilis

SpoIIE is a bifunctional protein involved in asymmetric septum formation and in activation of the forespore compartment-specific transcription factor σF through dephosphorylation of SpoIIAA-P. The phosphatase activity of SpoIIE requires Mn2+ as a metal cofactor. Here, we show that the presence of a metal cofactor also influences SpoIIE oligomerization and asymmetric septum formation. Absence of Mn2+ from sporulation medium results in a delay of the formation of polar FtsZ-rings, similar to a spoIIE null mutant. We purified the entire cytoplasmic part of the SpoIIE protein, and show that the protein copurifies with bound metals. Metal binding both stimulates SpoIIE oligomerization, and results in the formation of larger oligomeric structures. The presence of SpoIIE oligomers reduces FtsZ GTP hydrolysis activity and stabilizes FtsZ polymers in a light scattering assay. Combined, these results indicate that metal binding is not just required for SpoIIE phosphatase activity but also is important for SpoIIE's role in asymmetric septum formation.
Amyloid Imaging with 18F-Florbetaben in Alzheimer Disease and Other Dementias

Amyloid imaging with 18F-labeled radiotracers will allow widespread use, facilitating research, diagnosis, and therapeutic development for Alzheimer disease. The purpose of the study program was to compare cortical amyloid deposition using 18F-florbetaben and PET in controls and subjects with mild cognitive impairment (MCI), frontotemporal lobar degeneration (FTLD), dementia with Lewy bodies (DLB), vascular dementia (VaD), Parkinson disease (PD), and Alzheimer disease (AD). Methods: One hundred nine subjects in 3 clinical studies at Austin Health were reviewed: 32 controls, 20 subjects with MCI, and 30 patients with AD, 11 with FTLD, 7 with DLB, 5 with PD, and 4 with VaD underwent PET after intravenous injection of 300 MBq of 18F-florbetaben. Standardized uptake value ratios (SUVR) using the cerebellar cortex as a reference region were calculated between 90 and 110 min after injection. Results: When compared with the other groups, AD patients demonstrated significantly higher SUVRs (P < 0.0001) in neocortical areas. Most AD patients (96%) and 60% of MCI subjects showed diffuse cortical 18F-florbetaben retention. In contrast, only 9% of FTLD, 25% of VaD, 29% of DLB, and no PD patients and 16% of controls showed cortical binding. Although there was a correlation between Mini Mental State Examination and β-amyloid burden in the MCI group, no correlation was observed in controls, FTLD or AD. Conclusion: 18F-florbetaben had high sensitivity for AD, clearly distinguished patients with FTLD from AD, and provided results comparable to those reported with 11C-Pittsburgh Compound B in a variety of neurodegenerative diseases.
CURRENT STATUS AND FUTURE PERSPECTIVE OF ENDOSCOPIC DIAGNOSIS AND TREATMENT FOR COLORECTAL NEOPLASIA – SITUATION IN TAIWAN

The incidence of colorectal cancer (CRC) is rising substantially in Taiwan. Hence, both effective screening and management of colorectal neoplasms, including precursor lesions and early cancers, have become critically important. Colorectal cancer is not only curable, but also can be managed endoscopically if detected at the stage of precursor lesions or early cancer. Optimal management of colorectal neoplasia relies largely on accurate evaluation of the characteristics of lesions, including malignant transformation, and the depth of invasion of the malignant lesions. In this context, observation using image enhancing endoscopy (IEE) to magnify the image during colonoscopy is of utmost importance. Polypectomy or endoscopic mucosal resection is now the standard procedure for the treatment of colorectal adenoma or early cancerous lesions in Taiwan. Endoscopic submucosal dissection (ESD) is performed at only a few institutions; its long‐term efficacy and cost‐effectiveness require further elucidation. More attention from the government, academic societies, and individual clinicians is necessary.
Predicting pseudoknotted structures across two RNA sequences

Abstract Motivation: Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity. Results: A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support. Availability: DotKnot-PW and the RNA structure test set are available at the web site http://dotknot.csse.uwa.edu.au/pw. Contact: janaspe@csse.uwa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
Characterization of Perineural Invasion As a Component of Colorectal Cancer Staging

Perineural invasion (PN) in colorectal cancer (CRC) is a site-specific prognostic marker, as mentioned by the AJCC Cancer Staging Manual, but it remains to be clearly defined. We aimed to identify an optimal characterization of PN as a component of cancer staging. On the basis of the anatomic features of the nervous system of the large bowel, site-specific pathologic criteria were assigned to PN according to the location of PN. Multi-institutional pathologic review based on these criteria was performed for 962 patients with stage I to III CRC at 2 institutions (1999 to 2004, cohort 1) and 1883 patients from 8 other institutions (2000 to 2004, cohort 2). In cohort 1, intramural and extramural PN were observed in 152 and 101 patients, respectively, which had a different impact on disease-free survival (hazard ratio, 2.6 [1.9 to 3.5] vs. 4.7 [3.4 to 6.5], respectively). A 3-tiered grading system (Pn0; Pn1a, intramural PN; Pn1b, extramural PN) distinguished 5-year disease-free survival as 88%, 70%, and 48%, respectively; and multivariate analysis identified PN grade as a significant prognostic marker independent of T or N stage. These results were similar in cohort 2. Interinstitutional difference of the prognostic impact of PN grade was acceptably small among all institutions. Interobserver study among 6 gastrointestinal pathologists showed superior judgment reproducibility for PN compared with vascular invasion. The results of our study indicate that PN is an important prognostic marker in CRC. The value of cancer staging could be enhanced by PN assessment using site-specific criteria and a simple grading system based on PN location within the bowel.
Time Series Compressibility and Privacy

In this paper we study the trade-offs between time series compressibility and partial information hiding and their fundamental implications on how we should introduce uncertainty about individual values by perturbing them. More specifically, if the perturbation does not have the same compressibility properties as the original data, then it can be detected and filtered out, reducing uncertainty. Thus, by making the perturbation "similar" to the original data, we can both preserve the structure of the data better, while simultaneously making breaches harder. However, as data become more compressible, a fraction of the uncertainty can be removed if true values are leaked, revealing how they were perturbed. We formalize these notions, study the above trade-offs on real data and develop practical schemes which strike a good balance and can also be extended for on-the-fly data hiding in a streaming environment.
Determinants of Quality of Life in the Acute Stage Following Stroke

Objective This study aimed to investigate the factors influence the quality of life (QOL) of survivors of an acute stroke. Methods For 422 stroke patients, assessments were made within two weeks of the index event. QOL was measured using the World Health Organization Quality of Life-Abbreviated form (WHOQOL-BREF), which has four domains related to physical factors, psychological factors, social relationships, and environmental context. Associations of each four WHOQOL-BREF domain score with socio-demographic characteristics (age, sex, education, marital status, religion, and occupation), stroke severity (National Institutes of Health Stroke Scale), physical disability (Barthel Index), cognitive function (Mini-Mental Status Examination: MMSE), grip strength, and psychological distress (Hospital Anxiety and Depression Scale depression and anxiety subscale: HADS-D and HADS-A) were investigated using the linear regression models. Results Higher physical domain scores were independently associated with higher MMSE scores, stronger hand-grip strength, and lower HADS-D and HADS-A scores; higher psychological domain scores were independently associated with higher educational level, higher MMSE scores, and lower HADS-D and HADS-A scores; higher social relationships domain scores were independently associated with lower HADS-D and HADS-A scores; and higher environmental domain scores were independently associated with higher educational level, higher MMSE scores, and lower HADS-D scores. Conclusion Psychological distress and impaired cognitive function were independently associated with lower QOL in patients with acute stroke. However, stroke severity, physical disability and other socio-demographic factors were less significantly associated with QOL. These findings underscore the importance of psychological interventions for improving QOL during the acute phase following stroke.
PTask: operating system abstractions to manage GPUs as compute devices

We propose a new set of OS abstractions to support GPUs and other accelerator devices as first class computing resources. These new abstractions, collectively called the PTask API, support a dataflow programming model. Because a PTask graph consists of OS-managed objects, the kernel has sufficient visibility and control to provide system-wide guarantees like fairness and performance isolation, and can streamline data movement in ways that are impossible under current GPU programming models. Our experience developing the PTask API, along with a gestural interface on Windows 7 and a FUSE-based encrypted file system on Linux show that the PTask API can provide important system-wide guarantees where there were previously none, and can enable significant performance improvements, for example gaining a 5× improvement in maximum throughput for the gestural interface.
Land Use Affects Carbon Sources to the Pelagic Food Web in a Small Boreal Lake

Small humic forest lakes often have high contributions of methane-derived carbon in their food webs but little is known about the temporal stability of this carbon pathway and how it responds to environmental changes on longer time scales. We reconstructed past variations in the contribution of methanogenic carbon in the pelagic food web of a small boreal lake in Finland by analyzing the stable carbon isotopic composition (δ13C values) of chitinous fossils of planktivorous invertebrates in sediments from the lake. The δ13C values of zooplankton remains show several marked shifts (approx. 10 ‰), consistent with changes in the proportional contribution of carbon from methane-oxidizing bacteria in zooplankton diets. The results indicate that the lake only recently (1950s) obtained its present state with a high contribution of methanogenic carbon to the pelagic food web. A comparison with historical and palaeobotanical evidence indicates that this most recent shift coincided with agricultural land-use changes and forestation of the lake catchment and implies that earlier shifts may also have been related to changes in forest and land use. Our study demonstrates the sensitivity of the carbon cycle in small forest lakes to external forcing and that the effects of past changes in local land use on lacustrine carbon cycling have to be taken into account when defining environmental and ecological reference conditions in boreal headwater lakes.
Comparison of Milk-clotting Activity of Proteinase Produced by Bacillus Subtilis var, natto and Rhizopus oligosporus with Commercial Rennet

This study investigated purification and milk-clotting activity of the enzymes produced by Bacillus subtilis var, natto and Rhizopus oligosporus compared with that of commercial rennet. The clotting time, viscosity, tension and microstructure of the curd and electrophoretic patterns of milk proteins were determined. The milk-clotting activity/proteolytic activity ratios (MCA/PA ratio) of B. subtilis, R. oligosporus and commercial rennet were also compared. The results revealed that the curd formed by the commercial rennet had the highest viscosity and curd tension and the shortest clotting time among the three enzymes. However, curd produced by Rhizopus enzymes was ranked as second. From the MCA/PA ratio and electrophoretogram analyses it could be concluded that the enzyme produced by B. subtilis had the highest proteolytic activity, while the commercial rennet had the highest milk-clotting activity. Observations of microstructures of SEM showed that the three-dimensional network for curd formed by commercial rennet was denser, firmer and more smooth. The milk-clotting activity, specific activity, purification ratio and recovery of the purified enzymes produced by both the tested organisms were also determined with ion exchange chromatography and gel filtration.
Cloning by accident: an empirical study of source code cloning across software systems

One of the key goals of open source development is the sharing of knowledge, experience, and solutions that pertain to a software system and its problem domain. Source code cloning is one way in which expertise can be reused across systems; cloning is known to have been used in several open source projects, such as the SCSI drivers of the Linux kernel. In this paper, we discuss two case studies in which we performed clone detection on several open source systems within the same domain. In the first case study we examined nine text editors written in C, and in the second study we examined eight X-Windows window managers written in C and C++. To our surprise, we found little evidence of "true" cloning activity, but we did notice a significant number of "accidental" clones - that is, code fragments that are similar due to the precise protocols they must use when interacting with a given API or set of libraries. We further discuss the nature of "true" versus "accidental" clones, as well as the details of our case studies.
Usage-based vs. rule-based learning: the acquisition of word order in wh-questions in English and Norwegian

ABSTRACT This paper discusses different approaches to language acquisition in relation to children's acquisition of word order in wh-questions in English and Norwegian. While generative models assert that children set major word order parameters and thus acquire a rule of subject–auxiliary inversion or generalized verb second (V2) at an early stage, some constructivist work argues that English-speaking children are simply reproducing frequent wh-word+auxiliary combinations in the input. The paper questions both approaches, re-evaluates some previous work, and provides some further data, concluding that the acquisition of wh-questions must be the result of a rule-based process. Based on variation in adult grammars, a cue-based model to language acquisition is presented, according to which children are sensitive to minor cues in the input, called micro-cues. V2 is not considered to be one major parameter, but several smaller-scale cues, which are responsible for children's lack of syntactic (over-)generalization in the acquisition process.
Preliminary consideration of voltage stability impacts of geomagnetically induced currents

This paper provides a preliminary consideration of the voltage stability aspects of geomagnetically induced currents (GICs). Since the underlying geomagnetic disturbances (GMDs) can have rise times of less than one minute, there is a need to consider their impact on power system short-term voltage stability. The paper shows that the assumed dynamic models for loads and network controls such as load tap changing transformers (LTCs) can significantly reduce the GICs needed to cause a voltage collapse. Therefore more detailed dynamic simulations are recommended for inclusion in GIC studies.
Water Contact Angles on Poly(ethylene terephthalate) Film Exposed to Atmospheric Pressure Plasma

The poly(ethylene terephthalate), PET, film was exposed to atmospheric pressure plasma under various plasma processing parameters. The wettability of the PET film immediately after the exposure and after storage in air, which was determined by the sessile drop method, was strongly dependent on the plasma processing parameters. The contact angle hysteresis on the plasma-exposed PET film was examined by the Wilhelmy method. It was found that the hydrophobic recovery of the PET surface on storage after the plasma exposure was observed only for the advancing contact angle and that the receding angle remained almost the same. These experimental findings were explained on the basis of the calculation by Johnson and Dettre for the advancing and receding contact angles on model heterogeneous surfaces.
Multiple Zoonotic Parasites Identified in Dog Feces Collected in Ponte de Lima, Portugal — A Potential Threat to Human Health

Dogs play many roles and their presence within people’s houses has increased. In rural settings dog faeces are not removed from the streets, representing an environmental pollution factor. Our aim was to evaluate the occurrence of environmental contamination with zoonotic intestinal parasites of three groups of dogs in Ponte de Lima, Portugal, with a particular emphasis on Echinococcus granulosus. We collected 592 dog faecal samples from the environment, farm and hunting dogs. Qualitative flotation coprological analysis was performed and the frequency in the positive samples ranged between 57.44% and 81.19% in different groups. We isolated up to four different parasites in one sample and detected seven intestinal parasitic species, genera or families overall. Ancylostomatidae was the most prevalent parasite, followed by Trichuris spp. , Toxocara spp. , Isospora spp. , Dipylidium caninum, Taeniidae and Toxascaris leonina. Taeniidae eggs were analyzed with the PCR technique and revealed not to be from Echinococcus. The parasite prevalence and the diversity of zoonotic parasites found were high, which calls for a greater awareness of the problem among the population, especially hunters. Promoting research at the local level is important to plan control strategies. Health education should be developed with regard to farmers and hunters, and a closer collaboration between researchers, practitioners and public health authorities is needed.