LLukas22/scidocs huggingface dataset:
Learning Generative End-to-end Dialog Systems with Knowledge

Dialog systems are intelligent agents that can converse with human in natural language and facilitate human. Traditional dialog systems follow a modular approach and often have trouble expanding to new or more complex domains, which hinder the development of more powerful future dialog systems. This dissertation targets at an ambitious goal: to create domainagnostic learning algorithms and dialog models that can continuously learn to converse in any new domains and only requires a small amount of new data for the adaption. Achieving this goal first requires powerful statistic models that are expressive enough to model the natural language and decision-making process in dialogs of many domains; and second requires a learning framework enabling models to share knowledge from previous experience so it can learn to converse in new domains with limited data. End-to-end (E2E) generative dialog models based on encoder-decoder neural networks are strong candidates for the first requirement. The basic idea is to use an encoder network to map a dialog context into a learned distributed representation and then use a decoder network to generate the next system response. These models are not restricted to hand-crafted intermediate states and can in principle generalize to novel system responses that are not observed in the training. However, it is far from trivial to build a full-fledged dialog system using encoder-decoder models. Thus in the first stage of this thesis, we develop a set of novel neural network architectures that offer key properties that are required by dialog modeling. Experiments prove that the resulting system can interact with both users and symbolic knowledge bases, model complex dialog policy and reason over long discourse history. We tackle the second requirement by proposing a novel learning with knowledge (LWK) framework that can adapt the proposed system to new domains with minimum data. Two types of knowledge are studied: 1) domain knowledge from human experts 2) models' knowledge from learning related domains. To incorporate these knowledge, a domain description that can compactly encode domain knowledge is first proposed. Then we develop novel domain-aware models and training algorithms to teach the system learn from data in related domains and generalize to unseen ones. Experiments show the proposed framework is able to achieve strong performance in new domains with limited, even zero, in-domain training data. In conclusion, this dissertation shows that by combing specialized encoderdecoder models with the proposed LWK framework, E2E generative dialog models can be readily applied in complex dialog applications and can be easily expanded to new domains with extremely limited resources, which we believe is an important step towards future general-purpose conversational agents that are more natural and intelligent. November 21, 2017 DRAFT November 21, 2017 DRAFT
Formaldehyde exposure of medical students and instructors and clinical symptoms during gross anatomy laboratory in Thammasat University.

To study formaldehyde concentrations in the breathing zone and symptoms induced by gaseous formaldehyde exposure of medical students and instructors during gross anatomy laboratory at faculty of Medicine, Thammasat university. Formaldehyde concentrations in the indoor air and breathing zone of medical students were measured during the cadaver dissection. Formaldehyde concentrations in the indoor air and in the breathing zone were ranged from 0.401 to 0.581 ppm (mean 0.491 +/- 0.090) and from 0.472 to 0.848 ppm (mean 0.660 +/- 0.188) respectively. The mean of formaldehyde concentrations in the breathing zone of medical students and instructors was significantly higher than the mean of formaldehyde concentration in indoor air (p < 0.05). The most symptoms were general fatigue (82.7-87.8%), burning eyes (66.2-85.0%) and burning nose (62.5-81.1%). There was no statistically significant difference in burning eye symptom between contact lenses users and no contact lenses users (p > 0.05). Even though formaldehyde concentrations were relatively low, medical students, instructors and cadaver related workers should wear personal protective devices to reduce the effect of gaseous formaldehyde exposure during gross anatomy laboratory or contact cadaver.
In vivo validation of a catheter-based near-infrared spectroscopy system for detection of lipid core coronary plaques: initial results of the SPECTACL study.

OBJECTIVES
To determine whether catheter-based near-infrared spectroscopy (NIRS) signals obtained with a novel catheter-based system from coronaries of patients are similar to those from autopsy specimens and to assess initial safety of NIRS device.


BACKGROUND
An intravascular NIRS system for detection of lipid core-containing plaques (LCP) has been validated in human coronary autopsy specimens. The SPECTACL (SPECTroscopic Assessment of Coronary Lipid) trial was a parallel first-in-human multicenter study designed to demonstrate the applicability of the LCP detection algorithm in living patients.


METHODS
Intracoronary NIRS was performed in patients undergoing percutaneous coronary intervention. Acquired spectra were blindly compared with autopsy NIRS signals with multivariate statistics. To meet the end point of spectral similarity, at least two-thirds of the scans were required to have >80% of spectra similar to the autopsy spectra.


RESULTS
A total of 106 patients were enrolled; there were no serious adverse events attributed to NIRS. Spectroscopic data could not be obtained in 17 (16%) patients due to technical limitations, leaving 89 patients for analysis. Spectra from 30 patients were unblinded to test the calibration of the LCP detection algorithm. Of the remaining 59 blinded cases, after excluding 11 due to inadequate data, spectral similarity was demonstrated in 40 of 48 spectrally adequate scans (83% success rate, 95% confidence interval: 70% to 93%, median spectral similarity/pullback: 96%, interquartile range 10%). The LCP was detected in 58% of 60 spectrally similar scans from both cohorts.


CONCLUSIONS
This intravascular NIRS system safely obtained spectral data in patients that were similar to those from autopsy specimens. These results demonstrate the feasibility of invasive detection of coronary LCP with this novel system. (SPECTACL: SPECTroscopic Assessment of Coronary Lipid; NCT00330928).
Knowledge, Attitudes, and Willingness Toward Organ Donation Among Health Professionals in China.

BACKGROUND
The purposes of this study were to assess the knowledge, attitudes, and willingness toward organ donation among the health professionals in China.


METHODS
Questionnaires were delivered to 400 health professionals from 7 hospitals in Dalian and 1 hospital in Chaozhou of China between October 2013 and January 2014.


RESULTS
In all, 400 health professionals were approached, 373 valid responses were returned. Over 90% of the participants knew about organ donation, but only 17.4% had taken part in some training courses or lectures about organ donation. Health professionals (64.9%) knew the shortage status of organ, and doctors knew more than nurses and nonclinical staffs (P < 0.01). Health professionals (97.3%) knew brain death, and 68.9% professionals thought brain death was the reasonable criteria to judge death. Doctors showed a higher knowledge level about brain death than nurses and nonclinical staffs (P < 0.01). Altogether, 60.1% approved deceased donation; however, only 48.5% approved living donation. Doctors' attitudes were more positive than nurses and nonclinical both in deceased donation (P < 0.01) and in living donation (P < 0.05). In all, 49.3% were willing to donate their own organs postmortem, and doctors had higher willingness to donation postmortem compared with nurses and nonclinical staffs (P < 0.01). The most (49.2%) commonly cited reason for refraining from donation was: "afraid that organs would be picked up inhumanely and body would be disfigured".


CONCLUSIONS
Health professionals showed lower favorable attitudes and willingness toward organ donation than Chinese general public. A proportion of Chinese health professionals' knowledge about organ donation was limited.
Ambulatory photodynamic therapy using low irradiance inorganic light-emitting diodes for the treatment of non-melanoma skin cancer: an open study.

BACKGROUND/PURPOSE
Conventional photodynamic therapy (PDT) can be inconvenient and uncomfortable. We studied low irradiance PDT using an ambulatory inorganic light-emitting diode.


METHODS
Fifty-three patients with 61 lesions [superficial basal cell carcinoma (n = 30), Bowen's disease (n = 30), and actinic keratosis (AK; n = 1)] were studied. Two treatments of ambulatory PDT were undertaken 1 week apart (one treatment for AK). Clinical response was determined at 3 months, and the treatment cycle was repeated if there was residual disease. The endpoints assessed were pain during treatment (numerical rating scale (NRS); 0-10) and outcome at 1 year. Twenty-three of these patients also received conventional PDT to separate lesions.


RESULTS
The median NRS pain scores during first and second treatment were 2 (range 0-9) and 4 (0-9), respectively. Lesion clearance rate at 1 year after ambulatory PDT was 84% (21/25 lesions in 22 patients). Of the twenty-three patients treated with both ambulatory and conventional PDT, the median NRS was 1 (0-7) and 5 (1.5-9), respectively, with most patients preferring ambulatory PDT.


CONCLUSION
Ambulatory PDT is effective for superficial non-melanoma skin cancer, with 1 year clearance rates comparative to conventional PDT. Low irradiance ambulatory PDT may be less painful and more convenient than conventional PDT.
Common genetic polymorphisms of microRNA biogenesis pathway genes and breast cancer survival

Although the role of microRNA’s (miRNA’s) biogenesis pathway genes in cancer development and progression has been well established, the association between genetic variants of this pathway genes and breast cancer survival is still unknown. We used genotype data available from a previously conducted case–control study to investigate association between common genetic variations in miRNA biogenesis pathway genes and breast cancer survival. We investigated the possible associations between 41 germ-line single-nucleotide polymorphisms (SNPs) and both disease free survival (DFS) and overall survival (OS) among 488 breast cancer patients. During the median follow-up of 6.24 years, 90 cases developed disease progression and 48 cases died. Seven SNPs were significantly associated with breast cancer survival. Two SNPs in AGO2 (rs11786030 and rs2292779) and DICER1 rs1057035 were associated with both DFS and OS. Two SNPs in HIWI (rs4759659 and rs11060845) and DGCR8 rs9606250 were associated with DFS, while DROSHA rs874332 and GEMIN4 rs4968104 were associated with only OS. The most significant association was observed in variant allele of AGO2 rs11786030 with 2.62-fold increased risk of disease progression (95% confidence interval (CI), 1.41-4.88) and in minor allele homozygote of AGO2 rs2292779 with 2.94-fold increased risk of death (95% CI, 1.52-5.69). We also found cumulative effects of SNPs on DFS and OS. Compared to the subjects carrying 0 to 2 high-risk genotypes, those carrying 3 or 4–6 high-risk genotypes had an increased risk of disease progression with a hazard ratio of 2.16 (95% CI, 1.18- 3.93) and 4.47 (95% CI, 2.45- 8.14), respectively (P for trend, 6.11E-07). Our results suggest that genetic variants in miRNA biogenesis pathway genes may be associated with breast cancer survival. Further studies in larger sample size and functional characterizations are warranted to validate these results.
The Design and Application of RFID Tag System for Logistical Unit

At present, RFID is used in some practical fields such as supply chain management, stock management, and so on. However, for the cost reason, the RFID tags are not suitable for individual items, especially for lower-priced goods. In this paper, firstly, the features of logistical unit in the distribution are characterized, and its information is abstracted into a "tree" data structure. Secondly the logistical unit with the tags according with ISO-15693 is identified by using the SGTIN-96 and SSCC-96. Based on this, a scheme using the mix of RFID and barcode to reduce the cost is further proposed. Lastly, a tag operation module (TOM), which maintenances the data saved in the tag by establishing the index data in it, is introduced. According to the test, the effective operations of the RFID tag can be realized via TOM.
Decision making under ambiguity but not under risk is related to problem gambling severity

The aim of the present study was to examine the relationship between problem gambling severity and decision-making situations that vary in two degrees of uncertainty (probability of outcome is known: decision-making under risk; probability of outcome is unknown: decision-making under ambiguity). For this purpose, we recruited 65 gamblers differing in problem gambling severity and 35 normal controls. Decision-making under ambiguity was assessed with the Iowa Gambling Task (IGT) and the Card Playing Task (CPT). Decision-making under risk was assessed with the Coin Flipping Task (CFT) and the Cups Task. In addition, we included an examination of two working memory components (verbal storage and dual tasking). Results show that problem gamblers performed worse than normal controls on both ambiguous and risky decision-making. Higher problem gambling severity scores were associated with poorer performance on ambiguous decision-making tasks (IGT and CPT) but not decision-making under risk. Additionally, we found that dual task performance correlated positively with decision-making under risk (CFT and Cups tasks) but not with decision-making under ambiguity (IGT and CPT). These results suggest that impairments in decision-making under uncertain conditions of problem gamblers may represent an important neurocognitive mechanism in the maintenance of their problem gambling.
The Foundations of Literacy Development in Children at Familial Risk of Dyslexia

The development of reading skills is underpinned by oral language abilities: Phonological skills appear to have a causal influence on the development of early word-level literacy skills, and reading-comprehension ability depends, in addition to word-level literacy skills, on broader (semantic and syntactic) language skills. Here, we report a longitudinal study of children at familial risk of dyslexia, children with preschool language difficulties, and typically developing control children. Preschool measures of oral language predicted phoneme awareness and grapheme-phoneme knowledge just before school entry, which in turn predicted word-level literacy skills shortly after school entry. Reading comprehension at 8½ years was predicted by word-level literacy skills at 5½ years and by language skills at 3½ years. These patterns of predictive relationships were similar in both typically developing children and those at risk of literacy difficulties. Our findings underline the importance of oral language skills for the development of both word-level literacy and reading comprehension.
Sensitivity to change of AIMS2 and AIMS2-SF components in comparison to M-HAQ and VAS-pain.

OBJECTIVE
To examine sensitivity to change of Dutch versions of AIMS2 (arthritis impact measurement scales-2) and AIMS2-SF (short form) components, in comparison with M-HAQ (modified health assessment questionnaire) and the 100 mm visual analogue scale for pain (VAS-pain) in patients with rheumatoid arthritis.


METHODS
218 patients participated in a study on patient education. Participants completed the Dutch AIMS2, M-HAQ, and VAS-pain at baseline and after one year; 165 completed both assessments. The education programme did not have any effect on health status. Patients were classified according to change over one year in their responses to the AIMS2 question about general health perception: improved health (n = 32), no change (n = 101), and poorer health (n = 32). Changes in scores over one year were tested with paired t tests, and standardised response means were calculated for AIMS2 and AIMS2-SF components, M-HAQ total score, and VAS-pain in the three classifications of change in health perception.


RESULTS
AIMS2 and AIMS2-SF physical, symptom, and affect components showed similar sensitivity to change. The physical and symptom components performed better than M-HAQ and VAS-pain. AIMS2 and AIMS2-SF social interaction and role components were not sensitive to changes in general health perception. The role component was only applicable in 63 patients, because the others were unemployed, disabled, or retired.


CONCLUSIONS
AIMS2-SF is a good alternative to the AIMS2 long form for the assessment of health status in rheumatoid arthritis, and is preferable to M-HAQ and VAS-pain. Use of the AIMS2-SF makes it easier and less costly to collect data and reduces the burden on patients.
Sparsity regularization for image reconstruction with Poisson data

This work investigates three penalized-likelihood expectation maximization (EM) algorithms for image reconstruction with Poisson data where the images are known a priori to be sparse in the space domain. The penalty functions considered are the 1 norm, the 0 “norm,” and a penalty function based on the sum of logarithms of pixel values, R(x) = ∑np j=1 log (xj δ + 1 ) . Our results show that the 1 penalized algorithm reconstructs scaled versions of the maximum-likelihood (ML) solution, which does not improve the sparsity over the traditional ML estimate. Due to the singularity of the Poisson log-likelihood at zero, the 0 penalized EM algorithm is equivalent to the maximum-likelihood EM algorithm. We demonstrate that the penalty based on the sum of logarithms produces sparser images than the ML solution. We evaluated these algorithms using experimental data from a position-sensitive Compton-imaging detector, where the spatial distribution of photon-emitters is known to be sparse.
Learning Extraction Patterns for Subjective Expressions

This paper presents a bootstrapping process that learns linguistically rich extraction patterns for subjective (opinionated) expressions. High-precision classifiers label unannotated data to automatically create a large training set, which is then given to an extraction pattern learning algorithm. The learned patterns are then used to identify more subjective sentences. The bootstrapping process learns many subjective patterns and increases recall while maintaining high precision.
SemSearch: A Search Engine for the Semantic Web

Semantic search promises to produce precise answers to user queries by taking advantage of the availability of explicit semantics of information in the context of the semantic web. Existing tools have been primarily designed to enhance the performance of traditional search technologies but with little support for naive users, i.e., ordinary end users who are not necessarily familiar with domain specific semantic data, ontologies, or SQL-like query languages. This paper presents SemSearch, a search engine, which pays special attention to this issue by hiding the complexity of semantic search from end users and making it easy to use and effective. In contrast with existing semantic-based keyword search engines which typically compromise their capability of handling complex user queries in order to overcome the problem of knowledge overhead, SemSearch not only overcomes the problem of knowledge overhead but also supports complex queries. Further, SemSearch provides comprehensive means to produce precise answers that on the one hand satisfy user queries and on the other hand are self-explanatory and understandable by end users. A prototype of the search engine has been implemented and applied in the semantic web portal of our lab. An initial evaluation shows promising results.
Xenopus sonic hedgehog as a potential morphogen during embryogenesis and thyroid hormone-dependent metamorphosis

The hedgehog family of proteins have been implicated as important signaling molecules in establishing cell positional information and tissue patterning. Here we present the cloning and characterization of a hedgehog homologue from Xenopus laevis similar to the sonic class of vertebrate hedgehog genes. We isolated Xenopus hedgehog (Xhh) from a subtractive hybridization screen designed to identify genes induced by thyroid hormone during metamorphosis of the X.laevis gastrointestinal tract. In the intestine, Xhh mRNA expression was up-regulated at the climax of metamorphosis (stage 62) when intestinal epithelium underwent morphogenesis. Treatment of pre-metamorphic tadpoles with exogenous thyroid hormone (TH) resulted in a similar pattern of Xhh induction. Furthermore, TH induction was resistant to inhibitors of protein synthesis suggesting that Xhh is a direct thyroid hormone response gene. The expression and TH regulation of Xhh was not limited to the intestine, but was also observed in the limb and a mixture of pancreas and stomach. Throughout development, Xhh mRNA was present at varying levels with the earliest expression being detected at neurula stage. The highest levels of Xhh were observed between stages 33 and 40 shortly before tadpole feeding begins. Whole mount in situ hybridization analysis of Xhh expression in pre-hatching, stage 32 tadpoles demonstrated staining in the notochord and floor plate similar to that observed for other vertebrate hedgehog genes. Together, these data suggest a putative role for Xhh in organ development during both amphibian embryogenesis and metamorphosis.
Incidence rate and risk factors for vaginal vault prolapse repair after hysterectomy

Our objective was to estimate the incidence and identify the risk factors for vaginal vault prolapse repair after hysterectomy. We conducted a case control study among 6,214 women who underwent hysterectomy from 1982 to 2002. Cases (n = 32) were women who required vaginal vault suspension following the hysterectomy through December 2005. Controls (n = 236) were women, randomly selected from the same cohort, who did not require pelvic organ prolapse surgery. The incidence of vaginal vault prolapse repair was 0.36 per 1,000 women-years. The cumulative incidence was 0.5%. Risk factors included preoperative prolapse (odds ratio (OR) 6.6; 95% confidence interval (CI) 1.5–28.4) and sexual activity (OR 1.3; 95% CI 1.0–1.5). Vaginal hysterectomy was not a risk factor when preoperative prolapse was taken into account (OR 0.9; 95% CI 0.5–1.8).Vaginal vault prolapse repair after hysterectomy is an infrequent event and is due to preexisting weakness of pelvic tissues.