Miracle-dz/UniFAR-FTUs huggingface dataset:
Post-Specialisation: Retrofitting Vectors of Words Unseen in Lexical Resources

Word vector specialisation (also known as retrofitting) is a portable, light-weight approach to fine-tuning arbitrary distributional word vector spaces by injecting external knowledge from rich lexical resources such as WordNet. By design, these post-processing methods only update the vectors of words occurring in external lexicons, leaving the representations of all unseen words intact. In this paper, we show that constraint-driven vector space specialisation can be extended to unseen words. We propose a novel post-specialisation method that: a) preserves the useful linguistic knowledge for seen words; while b) propagating this external signal to unseen words in order to improve their vector representations as well. Our post-specialisation approach explicits a non-linear specialisation function in the form of a deep neural network by learning to predict specialised vectors from their original distributional counterparts. The learned function is then used to specialise vectors of unseen words. This approach, applicable to any post-processing model, yields considerable gains over the initial specialisation models both in intrinsic word similarity tasks, and in two downstream tasks: dialogue state tracking and lexical text simplification. The positive effects persist across three languages, demonstrating the importance of specialising the full vocabulary of distributional word vector spaces.
Creating a Framework for Experimentally Testing Early Visual Processing: A Response to Nurmoja, et al. (2012) on Trait Perception from Pixelized Faces

Nurmoja, Eamets, Härma, and Bachmann (2012) revealed that strongly pixelated pictures of faces still provide relevant cues for reliably assessing the apparent (i.e., subjectively perceived) traits of the portrayed. The present article responds to the paper by developing the outline of a framework for future research to reveal certain steps in processing complex visual stimuli. This framework combines the approach of degradation of the stimuli with the so-called microgenetic approach of percepts based on presentation time limitations. The proposed combination of a particular kind of stimulus manipulation and a specific experimental procedure allows testing targeted assumptions concerning visual processing, not only in the domain of face perception, but in all domains involving complex visual stimuli, for example, art perception.
Oral N-acetylcysteine reduces plasma homocysteine concentrations regardless of lipid or smoking status.

BACKGROUND Elevated total plasma homocysteine (tHcy) is considered to be an independent cardiovascular disease risk factor, although tHcy lowering by B-vitamins improves only certain clinical endpoints. N-acetylcysteine (NAC), a thiol-containing antioxidant, acutely lowers tHcy and possibly also blood pressure. However, to our knowledge, at present no conclusive long-term evaluation exists that controls for factors such as hyperlipidemia, smoking, medication, and disease stage, all of which affect the thiol redox state, including tHcy. OBJECTIVE We reanalyzed 2 double-blind, placebo-controlled trials in unmedicated middle-aged men, one in a hyperlipidemic group (HYL group; n = 40) and one in a normolipidemic group (NOL group; n = 42), each stratified for smokers and nonsmokers. DESIGN We evaluated the effect of 4 wk of oral NAC (1.8 g/d) on tHcy (primary endpoint), plasma thiol (cysteine), and intracellular glutathione concentrations as well as on blood pressure. The HYL group had total cholesterol >220 mg/dL or triglycerides >150 mg/dL. RESULTS NAC treatment significantly (P = 0.001, multivariate analysis of variance for repeated measures) lowered postabsorptive plasma concentrations of tHcy by -11.7% ± 3.0% (placebo: 4.1% ± 3.6%) while increasing those of cysteine by 28.1% ± 5.7% (placebo: 4.0% ± 3.4%) with no significant impact of hyperlipidemia or smoking. Moreover, NAC significantly decreased systolic (P = 0.003) and diastolic (P = 0.017) blood pressure within all subjects with a significant reduction in diastolic pressure in the HYL group (P = 0.008) but not in the NOL group. An explorative stepwise multiple regression analysis identified 1) post-treatment cysteine as well as 2) pretreatment tHcy and 3) albumin plasma concentrations as being significant contributors to tHcy reduction. CONCLUSIONS Four weeks of oral NAC treatment significantly decreased plasma tHcy concentrations, irrespective of lipid or smoking status, and lowered systolic blood pressure in both normolipidemic and hyperlipidemic men, with significant diastolic blood pressure reductions in the HYL group only. Increased oral intake of cysteine may therefore be considered for primary or secondary prevention of vascular events with regard to the 2 independent risk factors of hyperhomocysteinemia and arterial hypertension.
Establishment of a GIST-T1 gastrointestinal stromal tumour cell line resistant to imatinib mesylate

In the present study, imatinib mesylate (IM) was used to induce resistance in the gastrointestinal stromal tumour (GIST) cell line, GIST-T1, to establish a stable resistant cell line. The growth characteristics and expression profile of the established cell line were compared with those of the parental cell line. Additionally, the resistance mechanism of the gastrointestinal stromal tumours was preliminarily investigated. The GIST-T1 cells were cultured in vitro, and the drug was administered in the logarithmic phase of cell growth using intermittent dosing with increasing concentrations to obtain a drug-resistant cell line by repeated induction. Differences in the biological behaviours of the parental cells and drug-resistant cells were examined, and changes in the expression profiles were compared in the two cell lines. The results showed that the IM-resistant GIST-T1 cell line (GIST-T1 IR) was successfully established. Analysis of the biological behaviours of the two cell lines revealed that the average doubling times of the parental cells and drug-resistant cells were 26.59 and 33.63 h, respectively. The results of a scratch migration assay revealed that the migration ability was enhanced in the GIST-T1 IR cells. The results of CCK-8 detection indicated that the half maximal inhibitory concentration values of the two types of cells were 10.5 and 42.0 µM, respectively, which represented an increase of ~4-fold in the GIST-T1 IR cells. Flow cytometric cell cycle analysis indicated that the numbers of cells in the G0/G1, S and G2 phases increased following the induction treatment. Taken together, an IM-resistant GIST T1 cell line was successfully established, which opens novel avenues for individualized tumour chemotherapy.
Neuronal connections of direct and indirect pathways for stable value memory in caudal basal ganglia

Direct and indirect pathways in the basal ganglia work together for controlling behavior. However, it is still a controversial topic whether these pathways are segregated or merged with each other. To address this issue, we studied the connections of these two pathways in the caudal parts of the basal ganglia of rhesus monkeys using anatomical tracers. Our previous studies showed that the caudal basal ganglia control saccades by conveying long‐term values (stable values) of many visual objects toward the superior colliculus. In experiment 1, we injected a tracer in the caudate tail (CDt), and found local dense plexuses of axon terminals in the caudal‐dorsal‐lateral part of substantia nigra pars reticulata (cdlSNr) and the caudal‐ventral part of globus pallidus externus (cvGPe). These anterograde projections may correspond to the direct and indirect pathways, respectively. To verify this in experiment 2, we injected different tracers into cdlSNr and cvGPe, and found many retrogradely labeled neurons in CDt and, in addition, the caudal‐ventral part of the putamen (cvPut). These cdlSNr‐projecting and cvGPe‐projecting neurons were found intermingled in both CDt and cvPut (which we call “striatum tail”). A small but significant proportion of neurons (<15%) were double‐labeled, indicating that they projected to both cdlSNr and cvGPe. These anatomical results suggest that stable value signals (good vs. bad) are sent from the striatum tail to cdlSNr and cvGPe in a biased (but not exclusive) manner. These connections may play an important role in biasing saccades toward higher valued objects and away from lower valued objects.
Feature selection in UNSW-NB15 and KDDCUP'99 datasets

Machine learning and data mining techniques have been widely used in order to improve network intrusion detection in recent years. These techniques make it possible to automate anomaly detection in network traffics. One of the major problems that researchers are facing is the lack of published data available for research purposes. The KDD'99 dataset was used by researchers for over a decade even though this dataset was suffering from some reported shortcomings and it was criticized by few researchers. In 2009, Tavallaee M. et al. proposed a new dataset (NSL-KDD) extracted from the KDD'99 dataset in order to improve the dataset where it can be used for carrying out research in anomaly detection. The UNSW-NB15 dataset is the latest published dataset which was created in 2015 for research purposes in intrusion detection. This research is analysing the features included in the UNSW-NB15 dataset by employing machine learning techniques and exploring significant features (curse of high dimensionality) by which intrusion detection can be improved in network systems. Therefore, the existing irrelevant and redundant features are omitted from the dataset resulting not only faster training and testing process but also less resource consumption while maintaining high detection rates. A subset of features is proposed in this study and the findings are compared with the previous work in relation to features selection in the KDD'99 dataset.
ICTV Virus Taxonomy Profile: Togaviridae.

The Togaviridae is a family of small, enveloped viruses with single-stranded, positive-sense RNA genomes of 10-12 kb. Within the family, the genus Alphavirus includes a large number of diverse species, while the genus Rubivirus includes the single species Rubella virus. Most alphaviruses are mosquito-borne and are pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g. chikungunya virus and eastern equine encephalitis virus). Rubella virus is transmitted by respiratory routes among humans. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Togaviridae, which is available at www.ictv. global/report/togaviridae.
Epidemiology, Workload, and Performance of Major League Baseball Pitchers Placed on the Disabled List.

There is limited information on the effect of pitcher workload, pitch type, and performance of Major League Baseball pitchers placed on the disabled list (DL). This study evaluated demographic, performance, workload, and injury data of 330 Major League Baseball pitchers with 454 injuries who were placed on the DL during the 2014 and 2015 seasons. Upper extremity, lower extremity, core, hip/groin, and other injuries were analyzed, and injury year data were compared with career data as well as against other injury groups. Upper extremity injuries represented 60% of injuries and a mean of 61.4 (SE, 2.6) days on the DL, while lower extremity and core injuries each represented 14% of all injuries. Players with upper extremity injuries returned to play the same season at the lowest rate (67.3%). Starters pitched more mean innings per game (5.31 vs 5.14 innings, P=.012) and threw more mean pitches per game (85.9 vs 82.4 pitches, P=.003) the year of injury compared with their career. There was a decrease in mean fastball velocity (92.2 vs 91.6 mph, P<.001) and percentage of fastballs thrown (60.3% vs 58.5%, P<.001) the year of injury for all injuries. The authors found that upper extremity injuries are the most common, require the most time on the DL, and have the lowest same season return to play rate. Starters pitched significantly more innings and threw more pitches during the year of injury. Pitchers were found to have a decrease in fastball velocity and percentage of fastballs thrown during the year of injury. [Orthopedics. 2018; 41(3):178-183. ].
Using Longitudinal Social Media Analysis to Understand the Effects of Early College Alcohol Use

While college completion is predictive of individual career happiness and economic achievement, many factors, such as excessive alcohol usage, jeopardize college success. In this paper, we propose a method for analyzing large-scale, longitudinal social media timelines to provide fine-grained visibility into how the behaviors and trajectories of alcohol-mentioning students differ from their peers. Using propensity score stratification to reduce bias from confounding factors, we analyze the Twitter data of 63k college students over 5 years to study the effect of early alcohol usage on topics linked to college success. We find multi-year effects, including lower mentions of study habits, increased mentions of potentially risky behaviors, and decreases in mentions of positive emotions. We conclude with a discussion of social media data's role in the study of the risky behaviors of college students and other individual behaviors with long-term effects.
Chapter 2 Epidemiology of sarcopenia

• Based on the definitions of sarcopenia provided in the European Working group on Sarcopenia in Older People (EWGSOP) and International Working group on Sarcopenia criteria, 1–29% and 14–33% of individuals aged ≥65 years residing around a given region and care facilities, respectively, meet the criteria for sarcopenia. The prevalence of sarcopenia can be estimated at 6–12% from the large-scale studies.
Identifying Cancer Specific Driver Modules Using a Network-Based Method

Detecting driver modules is a key challenge for understanding the mechanisms of carcinogenesis at the pathway level. Identifying cancer specific driver modules is helpful for interpreting the different principles of different cancer types. However, most methods are proposed to identify driver modules in one cancer, but few methods are introduced to detect cancer specific driver modules. We propose a network-based method to detect cancer specific driver modules (CSDM) in a certain cancer type to other cancer types. We construct the specific network of a cancer by combining specific coverage and mutual exclusivity in all cancer types, to catch the specificity of the cancer at the pathway level. To illustrate the performance of the method, we apply CSDM on 12 TCGA cancer types. When we compare CSDM with SpeMDP and HotNet2 with regard to specific coverage and the enrichment of GO terms and KEGG pathways, CSDM is more accurate. We find that the specific driver modules of two different cancers have little overlap, which indicates that the driver modules detected by CSDM are specific. Finally, we also analyze three specific driver modules of BRCA, BLCA, and LAML intersecting with well-known pathways. The source code of CSDM is freely accessible at https://github.com/fengli28/CSDM.git.
The Role of Morningness and Endurance in Mood and Attention During Morning and Evening Hours

Abstract. This study aimed at testing the effects of morningness-eveningness and endurance on mood and selective attention during morning and evening hours. University students (N = 80) completed the Polish version of the Morningness-Eveningness Questionnaire, the Formal Characteristics of Behaviour-Temperament Inventory, and two testing sessions scheduled during the morning and evening hours. Each testing session consisted of completing the UWIST Mood Adjective Checklist composed of three scales: energetic arousal (EA), tense arousal (TA), and hedonic tone (HT), and a computerized visual search task. Without consideration of morningness and endurance, a time-of-day effect appeared in the visual attention but not in affect: participants were more accurate and faster in the evening than in the morning. Considering morningness and endurance, neither of them influenced the selective attention but they did influence mood. Morningness influenced diurnal variations in EA and HT in such a way that from morning t.
High spatial heterogeneity of two planktonic cnidarian species related to the variability of a shelf-slope front at short time scales

We investigated the variability in the mesoscale distribution of the siphonophore Muggiaea atlantica and the hydromedusa Aglaura hemistoma in relation to the rapid spatial oscillations of the shelf-slope front off the Catalan coast (NW Mediterranean). Three extensive surveys were carried out in spring at ten-day intervals. High variability in the position of the front resulted from the advection of low-salinity waters originating in the Gulf of Lions, mainly from the Rhone River runoff. High spatial variability in the distribution of the two species was closely related to the shifting positions of the front. Both species occurred on its inshore side in much higher abundances than on its offshore side, where they were scarce or absent. The front acts as a barrier limiting offshore displacement of these two cnidarians. Statistical analyses showed that bottom depth and salinity, as independent variables, were indicators of the signature and position of the front, explaining most of the variance in the distribution and abundance of the two species.
Low Estrogen Receptor (ER)–Positive Breast Cancer and Neoadjuvant Systemic Chemotherapy: Is Response Similar to Typical ER-Positive or ER-Negative Disease?

Objectives Pathologic complete response (pCR) rate after neoadjuvant chemotherapy was compared between 141 estrogen receptor (ER)-negative (43%), 41 low ER+ (13%), 47 moderate ER+ (14%), and 98 high ER+ (30%) tumors. Methods Human epidermal growth factor receptor 2-positive cases, cases without semiquantitative ER score, and patients treated with neoadjuvant endocrine therapy alone were excluded. Results The pCR rate of low ER+ tumors was similar to the pCR rate of ER- tumors (37% and 26% for low ER and ER- respectively, P = .1722) but significantly different from the pCR rate of moderately ER+ (11%, P = .0049) and high ER+ tumors (4%, P < .0001). Patients with pCR had an excellent prognosis regardless of the ER status. In patients with residual disease (no pCR), the recurrence and death rate were higher in ER- and low ER+ cases compared with moderate and high ER+ cases. Conclusions Low ER+ breast cancers are biologically similar to ER- tumors. Semiquantitative ER H-score is an important determinant of response to neoadjuvant chemotherapy.
Effect of Preheat Temperatures on Mechanical Properties and Polymerization Contraction Stress of Dental Composites

Objectives: The purpose of this study was to investigate the effect of preheat temperatures on polymerization contraction stress and mechanical properties of three resin composites. Methods: Three resin composites (Filtek Supreme XT, GC Kalore, and Gradia Direct X) at room temperature, 37°C, and 60°C were investigated. Stress development and maximum contraction stress of the composites were evaluated. Directly after preheating, samples were light-cured for 40 seconds and the force recorded for 15 minutes. Subsequent calculations were done to account for the system’s compliance and to obtain the shrinkage stress of the composites. In addition, composite discs (5 mm? and1 mmthick) were light-cured for 40 seconds at the preheat temperature. Hardness, elastic modulus, and creep of composites were investigated using a nano-indentation system (UMIS 2000). The results were analyzed using Two-way Analysis of Variance (2-way ANOVA) and Tukey’s Post-Hoc test (α = 0.05). Results: The results indicated that preheating composites to 37°C and 60°C increased the polymerization contraction forces, but did not significantly affect hardness, elastic modulus, and creep behaviour of the materials. Analysis of the contraction force upon allowing for thermal contraction indicated only a minor influence of preheat temperature. Significance: Preheating composites, upon allowing for system thermal contraction, showed a slight increase of the polymerization contraction stress but did not significantly affect the composites’ mechanical properties.
Circulating EBV DNA, Globulin and Nodal Size Predict Distant Metastasis after Intensity-Modulated Radiotherapy in Stage II Nasopharyngeal Carcinoma

Background: The optimal treatment for early-stage nasopharyngeal carcinoma (NPC) remains controversial. Identification of prognostic factors for metastasis and tumor progression is urgently required to improve clinical decision-making for patients with American Joint Committee on Cancer (AJCC) 2009 stage II NPC from the endemic area. Methods: Consecutive newly-diagnosed patients (n=296) with non-disseminated, biopsy-proven stage II NPC were retrospectively reviewed; all patients received intensity-modulated radiotherapy and MRI follow-up. Plasma EBV DNA level, serum lactate dehydrogenase, serum albumin, serum globulin and leukocyte counts were measured before therapy. Survival rates were analyzed using the Kaplan-Meier method and log-rank test and multivariate Cox proportional hazards model. Results: Median follow-up was 50.2 months (range, 8-69.5 months). Multivariate analysis demonstrated a plasma Epstein-Barr virus (EBV) DNA level ≥ 4000 copies/mL, maximal axial diameter (MAD) of the cervical lymph nodes ≥ 30 mm and serum globulin level < 29.5 g/L were independent predictors of poor DMFS (P = 0.018; P = 0.019; P = 0.006, respectively). On the basis of these parameters, a prognostic model was developed as follows: 1) patients with no risk factors; 2) one risk factor; and 3) two or three risk factors. The 3-year distant metastasis-free survival rates for groups 1, 2 and 3 were 100%, 94.6% and 84.3%, respectively (P = 0.001). Conclusion: The prognostic model based on EBV DNA, serum globulin and nodal size may facilitate individualized treatment of patients with stage II NPC at high risk of distant metastasis.
Analysis of Postoperative Recurrence in Stage I–III Midgut Neuroendocrine Tumors

Background Surgery represents the only curative treatment for stage I-III midgut neuroendocrine tumors (NETs). At present, there are very limited data on the risk of postoperative recurrence. The optimal modality, duration and frequency of surveillance have not been well established. In this work, we investigated the long-term risk of recurrence, peak timing of recurrence, and potential predictors of relapse in patients with stage I-III midgut NETs. Methods We retrospectively evaluated 129 patients with stage I-III midgut NETs who were seen at the Moffitt Cancer Center between 2000 and 2010 following an R0/R1 resection. Disease-free survival (DFS) was estimated using the Kaplan-Meier method. Demographic, clinical, and pathological features were assessed as potential predictors of recurrence. All statistical tests were two-sided. Results After a median postoperative follow-up of 81 months (range = 1-295 months), recurrence was diagnosed in 40 out of 129 patients (31.0%, 95% confidence interval [CI] = 23.0% to 39.0%). Liver, mesentery, and pelvic lymph nodes were the main sites of relapse. The median DFS was 138 months (95% CI = 117 to 223 months). Resection of 17 or fewer lymph nodes predicted relapse (P = .01) and shorter DFS (P = .04). Among patients who relapsed, the cumulative risks of recurrence at one, five, and 10 years were 15.0% (95% CI = 3.9% to 26.1%), 50.0% (95% CI = 34.5% to 65.5%), and 85.0% (95% CI = 73.9% to 96.0%). No recurrence was observed among patients (n = 6) with stage I tumors, whereas similar rates of relapse were noted in patients with stage II or III NETs (n = 118). Conclusions An annual surveillance interval may allow early detection of recurrence. Given the apparent decline in recurrence after eight years from surgery, a decade-long duration of active surveillance may be proposed.