Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal Effects of the Home Learning Environment and Parental Difficulties on Reading and Math Development Across Grades 1–9

This study focuses on parental reading and mathematical difficulties, the home literacy environment, and the home numeracy environment as well as their predictive role in Finnish children’s reading and mathematical development through Grades 1–9. We examined if parental reading and mathematical difficulties directly predict children’s academic performance and/or if they are mediated by the home learning environment. Mothers (n = 1590) and fathers (n = 1507) reported on their reading and mathematical difficulties as well as on the home environment (shared reading, teaching literacy, and numeracy) when their children were in kindergarten. Tests for reading fluency, reading comprehension, and arithmetic fluency were administered to children in Grades 1, 2, 3, 4, 7, and 9. Parental reading difficulties predicted children’s reading fluency, whereas parental mathematical difficulties predicted their reading comprehension and arithmetic fluency. Familial risk was associated with neither formal nor informal home environment factors, whereas maternal education had a significant relationship with both, with higher levels of education among mothers predicting less time spent on teaching activities and more time spent on shared reading. In addition, shared reading was significantly associated with the development of reading comprehension up to Grades 3 and 4, whereas other components of the home learning environment were not associated with any assessed skills. Our study highlights that taken together, familial risk, parental education, and the home learning environment form a complex pattern of associations with children’s mathematical and reading skills.
CryptoTutor: Teaching Secure Coding Practices through Misuse Pattern Detection

Insecure program practices seriously threaten software security. Misusing security primitives in application-level code is not unusual. For example, in mobile banking apps, developers might store customers' privacy information in plaintext, leading to sensitive information leakage. To leverage cryptographic primitives, developers need to correctly select the cryptographic algorithm, appropriate parameters, and sometimes its post-process. While recent research discusses pitfalls in cryptography-related implementations, few academic programs integrate these concepts in their educational programs. One big challenge is the lack of automated guidance on how to utilize existing libraries for secure coding. In this paper, we discuss the prevalence of the problem, especially with respect to implementing programs that utilize cryptography, to motivate the need for better tool support for guidance in writing secure code. We present a tool, CryptoTutor, that can automatically flag common cryptographic misuses and suggest possible repairs. We discuss how tools like CryptoTutor can be integrated into programming courses at the college and pre-college levels.
FairMixRep: Self-supervised Robust Representation Learning for Heterogeneous Data with Fairness constraints

Representation Learning in a heterogeneous space with mixed variables of numerical and categorical types has interesting challenges due to its complex feature manifold. Moreover, feature learning in an unsupervised setup, without class labels and a suitable learning loss function, adds to the problem complexity. Further, the learned representation and subsequent predictions should not reflect discriminatory behavior towards certain sensitive groups or attributes. The proposed feature map should preserve maximum variations present in the data and needs to be fair with respect to the sensitive variables. We propose, in the first phase of our work, an efficient encoder-decoder framework to capture the mixed-domain information. The second phase of our work focuses on de-biasing the mixed space representations by adding relevant fairness constraints. This ensures minimal information loss between the representations before and after the fairness-preserving projections. Both the information content and the fairness aspect of the final representation learned has been validated through several metrics where it shows excellent performance. Our work (FairMixRep) addresses the problem of Mixed Space Fair Representation learning from an unsupervised perspective and learns a Universal representation which is timely, unique and a novel research contribution. 11This paper is accepted at ICDM'2020 DLC Workshop.
Like Hiking? You Probably Enjoy Nature: Persona-grounded Dialog with Commonsense Expansions

Existing persona-grounded dialog models often fail to capture simple implications of given persona descriptions, something which humans are able to do seamlessly. For example, state-of-the-art models cannot infer that interest in hiking might imply love for nature or longing for a break. In this paper, we propose to expand available persona sentences using existing commonsense knowledge bases and paraphrasing resources to imbue dialog models with access to an expanded and richer set of persona descriptions. Additionally, we introduce fine-grained grounding on personas by encouraging the model to make a discrete choice among persona sentences while synthesizing a dialog response. Since such a choice is not observed in the data, we model it using a discrete latent random variable and use variational learning to sample from hundreds of persona expansions. Our model outperforms competitive baselines on the PersonaChat dataset in terms of dialog quality and diversity while achieving persona-consistent and controllable dialog generation.
Pkwrap: a PyTorch Package for LF-MMI Training of Acoustic Models

We present a simple wrapper that is useful to train acoustic models in PyTorch using Kaldi's LF-MMI training framework. The wrapper, called pkwrap (short form of PyTorch kaldi wrapper), enables the user to utilize the flexibility provided by PyTorch in designing model architectures. It exposes the LF-MMI cost function as an autograd function. Other capabilities of Kaldi have also been ported to PyTorch. This includes the parallel training ability when multi-GPU environments are unavailable and decode with graphs created in Kaldi. The package is available on Github at this https URL.
Quantum graphs -- Generic eigenfunctions and their nodal count and Neumann count statistics

In this thesis, we study Laplacian eigenfunctions on metric graphs, also known as quantum graphs. We restrict the discussion to standard quantum graphs. These are finite connected metric graphs with functions that satisfy Neumann vertex conditions. The first goal of this thesis is the study of the nodal count problem. That is the number of points on which the $n$th eigenfunction vanishes. We provide a probabilistic setting using which we are able to define the nodal count\textquoteright s statistics. We show that the nodal count statistics admit a topological symmetry by which the first Betti number of the graph can be obtained. We revise a conjecture that predicts a universal Gaussian behavior of the nodal count statistics for large graphs and we prove it for a certain family of graphs. The second goal is to formulate and study the Neumann count, which is the number of local extrema of the $n$th eigenfunction. This counting problem is motivated by the Neumann partitions of planar domains, a novel concept in spectral geometry. We provide uniform bounds on the Neumann count and investigate its statistics. We show that the Neumann count provides complimentary geometrical information to that obtained from the nodal count. We show that for a certain family of growing tree graphs the Neumann count statistics approaches a Gaussian distribution. The third goal is a genericity result, which justifies the generality of the Neumann count discussion. To this day it was known that generically, eigenfunctions do not vanish on vertices. We generalize this result to derivatives at vertices as well. That is, generically, the derivatives of an eigenfunction on interior vertices do not vanish.
Epilogues and last words in Shakespeare: Exploring patterns in a small corpus

This article considers the linguistic features of the speeches that end Shakespeare’s plays, some of which are formally labelled as Epilogues. It introduces a play’s last words as a type of paratext using the theoretical models devised by Genette (1997), and then considers the material evidence surrounding Epilogues, a specific form of last words, using research on their ephemeral and occasional nature by Stern (2009). The difficulties of using corpus methods in the case of small, specialist subcorpora of paratexts is then considered, and the methodology adopted to extract and present the results is outlined. The demonstrates features of the Last Words corpus: how pronouns raise questions about the speaker’s stance (with reference to work by Goffman (1979) and Messerli (2017)); how these speeches deploy the language of inclusivity; how they interpellate spectators or readers to promote a specific agenda. Because last words enact the fragile liminal moment where characters, actors and audience are united by their experience of the performance, the article considers their retrospective and prospective orientation. It demonstrates how the prominence of verbs like ‘shall’ and ‘will’ can be used for marketing purposes. The problems raised by uneven dispersion of terms are discussed leading to a case study of the Epilogue of As You Like It which demonstrates how its use of language is deliberately linked to the discursive world of the play which precedes it.
The Systematic Review and Meta-Analysis on the Immunogenicity and Safety of the Tuberculosis Subunit Vaccines M72/AS01E and MVA85A

Background: Tuberculosis (TB) is a severe infectious disease with devastating effects on global public health. No TB vaccine has yet been approved for use on latent TB infections and healthy adults. In this study, we performed a systematic review and meta-analysis to evaluate the immunogenicity and safety of the M72/AS01E and MVA85A subunit vaccines. The M72/AS01E is a novel peptide-based vaccine currently in progress, which may increase the protection level against TB infection. The MVA85A was a viral vector-based TB subunit vaccine being used in the clinical trials. The vaccines mentioned above have been studied in various phase I/II clinical trials. Immunogenicity and safety is the first consideration for TB vaccine development. Methods: The PubMed, Embase, and Cochrane Library databases were searched for published studies (until October 2019) to find out information on the M72/AS01E and MVA85A candidate vaccines. The meta-analysis was conducted by applying the standard methods and processes established by the Cochrane Collaboration. Results: Five eligible randomized clinical trials (RCTs) were selected for the meta-analysis of M72/AS01E candidate vaccines. The analysis revealed that the M72/AS01E subunit vaccine had an abundance of polyfunctional M72-specific CD4+ T cells [standardized mean difference (SMD) = 2.37] in the vaccine group versus the control group, the highest seropositivity rate [relative risk (RR) = 5.09]. The M72/AS01E vaccinated group were found to be at high risk of local injection site redness (RR = 2.64), headache (RR = 1.59), malaise (RR = 3.55), myalgia (RR = 2.27), fatigue (RR = 2.16), pain (RR = 3.99), swelling (RR = 5.09), and fever (RR = 2.04) compared to the control groups. The incidences of common adverse events of M72/AS01E were local injection site redness, headache, malaise, myalgia, fatigue, pain, swelling, fever, etc. Six eligible RCTs were selected for the meta-analysis on MVA85A candidate vaccines. The analysis revealed that the subunit vaccine MVA85A had a higher abundance of overall pooled proportion polyfunctional MVA85A-specific CD4+ T cells SMD = 2.41 in the vaccine group vs. the control group, with the highest seropositivity rate [estimation rate (ER) = 0.55]. The MVA85A vaccinated group were found to be at high risk of local injection site redness (ER = 0.55), headache (ER = 0.40), malaise (ER = 0.29), pain (ER = 0.54), myalgia (ER = 0.31), and fever (ER = 0.20). The incidences of common adverse events of MVA85A were local injection site redness, headache, malaise, pain, myalgia, fever, etc. Conclusion: The M72/AS01E and MVA85A vaccines against TB are safe and had immunogenicity in diverse clinical trials. The M72/AS01E and MVA85A vaccines are associated with a mild adverse reaction. The meta-analysis on immunogenicity and safety of M72/AS01E and MVA85A vaccines provides useful information for the evaluation of available subunit vaccines in the clinic.
Cellular and molecular studies of Mycoplasma pneumoniae adherence and gliding motility

Mycoplasmas are cell wall-less prokaryotes considered to be among the simplest known microorganisms capable of self-replication. Several mycoplasma species are distinguished by the presence of a complex assemblage of proteins comprising a differentiated terminal organelle containing a Triton X-100 insoluble electron-dense core. This terminal organelle is an extension of the mycoplasma cell and is thought to function in cell division, host cell interactions, and gliding motility. Through mutant analysis, several proteins have been found to be required for cytadherence and are components of the terminal organelle including HMW1-HMW3, P1, B, C, and P30. Protein P30 consists of a predicted signal sequence, cytoplasmic domain, membranespanning region, and extracellular proline-rich C-terminal domain. Protein P65 localizes to the terminal organelle, yet its role in cytadherence is unknown as no mutant lacking only P65 has been reported. Upon analysis of previously isolated cytadherence mutants and P30 structurefunction constructs created here and expressed in a P30 null mutant, we found that HMW1HMW3, and P30 are required for P65 stability and in the case of P30, stabilization was mediated by the surface-exposed and not cytoplasmic domain. In contrast, P65 localization only required HMW1-HMW3 and not P30. We examined gliding motility of M. pneumoniae using two assays we developed and found that cytadherence mutants absent of electron-dense cores (HMW1HMW2) were incapable of motility. Of the strains possessing electron-dense cores an intermediate level of gliding was seen in the absence of HMW3, and in strains having certain defects in the surface-exposed domain of P30. Despite the presence of electron-dense cores, no motility was seen in the absence of proteins B and C and in certain P30 mutants. P30 stability was most affected by deletion of a highly conserved region in the surface-exposed domain of P30 and although hemadsorption was the most sensitive phenotype to any alteration in the P30 sequence, a P30 revertant strain was isolated which exhibited wild-type levels of attachment to hamster respiratory epithelium yet only demonstrated an intermediate motility phenotype. Thus, this strain might be useful to determine if gliding motility is a virulence determinant for M. pneumoniae pathogenesis.
Topological electronic structure in the antiferromagnet HoSbTe

Magnetic topological materials, in which the time-reversal symmetry is broken, host various exotic quantum phenomena, including the quantum anomalous Hall effect, axion insulator states, and Majorana fermions. The study of magnetic topological materials is at the forefront of condensed matter physics. Recently, a variety of magnetic topological materials have been reported, such as ${\mathrm{Mn}}_{3}\mathrm{Sn}, {\mathrm{Co}}_{3}{\mathrm{Sn}}_{2}{\mathrm{S}}_{2}, {\mathrm{Fe}}_{3}{\mathrm{Sn}}_{2}$, and ${\mathrm{MnBi}}_{2}{\mathrm{Te}}_{4}$. Here, we report the observation of a topological electronic structure in an antiferromagnet, HoSbTe, a member of the ZrSiS family of materials, by angle-resolved photoemission spectroscopy (ARPES) measurements and first-principles calculations. We demonstrate that HoSbTe is a Dirac nodal line semimetal when spin-orbit coupling (SOC) is neglected. However, our theoretical calculations show that the strong SOC in HoSbTe fully gaps out the nodal lines and drives the system to a weak topological insulator state, with each layer being a two-dimensional topological insulator. Because of the strong SOC in HoSbTe, the gap is as large as hundreds of meV along specific directions, which is directly observed by our ARPES measurements. The existence of magnetic order and topological properties in HoSbTe makes it a promising material for the realization of exotic quantum devices.
NLRP3 and mTOR Reciprocally Regulate Macrophage Phagolysosome Formation and Acidification Against Vibrio vulnificus Infection

The marine bacterium Vibrio vulnificus causes potentially fatal bloodstream infections, typically in patients with chronic liver diseases. The inflammatory response and anti-bacterial function of phagocytes are crucial for limiting bacterial infection in the human hosts. How V. vulnificus affects macrophages after phagocytosis is unclear. In this report, we found that the bactericidal activity of macrophages to internalize V. vulnificus was dependent on mammalian target of rapamycin (mTOR) and NOD-like receptor (NLR) family pyrin domain containing 3 (NLRP3) interaction. Additionally, the NLRP3 expression was dependent on mTORC1 activation. Inhibited mTORC1 or absence of NLRP3 in macrophages impaired V. vulnificus-induced phagosome acidification and phagolysosome formation, leading to a reduction of intracellular bacterial clearance. mTORC1 signaling overactivation could increase NLRP3 expression and restore insufficient phagosome acidification. Together, these findings indicate that the intracellular bactericidal activity of macrophages responding to V. vulnificus infection is tightly controlled by the crosstalk of NLRP3 and mTOR and provide critical insight into the host bactericidal activity basis of clearance of V. vulnificus through lyso/phagosome.
An ethnographic exploration of the social organisation of general practice nurses’ knowledge use: more than ‘mindlines’?

Aim To explore contextual, organisational and educational issues impacting on access to, and application of knowledge to everyday practice by general practice nurses, working in two rural primary-care practices in the UK. Background Changes in primary-care healthcare delivery have resulted in substantive changes to practice nurses’ roles. Practice nurses have taken on enhanced roles for which they were not prepared for in their initial training, little is known about how they access and apply knowledge. Methods Ethnographic methods were used to gather data. Results Practice nurses take a blended approach to knowledge use, using elements of evidence-based practice to support professional judgement. This is subject to several contextual influences, organisational, educational and from individual patients. Tensions exist between the position in which general practice nurses are situated and the nature in which knowledge is disseminated and used in primary care. Whilst examples of clinical mindlines were evident, these differed to those previously observed in general practitioners, practice nurses did not always have the mindline on which to draw and used an approach to practice that resembled ‘bricoleur activity’. Conclusions The way in which general practice is structured results in variance in organisational structural arrangements for sharing and disseminating of knowledge. Despite a supportive organisational culture towards knowledge sharing, the position in which practice nurses are situated limits opportunities for discussion and reformulation of knowledge. Practice nurses are, however, prepared to adapt knowledge to meet the needs of individual patients.
Learning to Explain: Datasets and Models for Identifying Valid Reasoning Chains in Multihop Question-Answering

Despite the rapid progress in multihop question-answering (QA), models still have trouble explaining why an answer is correct, with limited explanation training data available to learn from. To address this, we introduce three explanation datasets in which explanations formed from corpus facts are annotated. Our first dataset, eQASC, contains over 98K explanation annotations for the multihop question answering dataset QASC, and is the first that annotates multiple candidate explanations for each answer. The second dataset eQASC-perturbed is constructed by crowd-sourcing perturbations (while preserving their validity) of a subset of explanations in QASC, to test consistency and generalization of explanation prediction models. The third dataset eOBQA is constructed by adding explanation annotations to the OBQA dataset to test generalization of models trained on eQASC. We show that this data can be used to significantly improve explanation quality (+14% absolute F1 over a strong retrieval baseline) using a BERT-based classifier, but still behind the upper bound, offering a new challenge for future research. We also explore a delexicalized chain representation in which repeated noun phrases are replaced by variables, thus turning them into generalized reasoning chains (for example: "X is a Y" AND "Y has Z" IMPLIES "X has Z"). We find that generalized chains maintain performance while also being more robust to certain perturbations.
Coordination and Consonance Between Interacting, Improvising Musicians

Joint action (JA) is ubiquitous in our cognitive lives. From basketball teams to teams of surgeons, humans often coordinate with one another to achieve some common goal. Idealized laboratory studies of group behavior have begun to elucidate basic JA mechanisms, but little is understood about how these mechanisms scale up in more sophisticated and open-ended JA that occurs in the wild. We address this gap by examining coordination in a paragon domain for creative joint expression: improvising jazz musicians. Coordination in jazz music subserves an aesthetic goal: the generation of a collective musical expression comprising coherent, highly nuanced musical structure (e.g., rhythm, harmony). In our study, dyads of professional jazz pianists improvised in a “coupled,” mutually adaptive condition, and an “overdubbed” condition that precluded mutual adaptation, as occurs in common studio recording practices. Using a model of musical tonality, we quantify the flow of rhythmic and harmonic information between musicians as a function of interaction condition. Our analyses show that mutually adapting dyads achieve greater temporal alignment and produce more consonant harmonies. These musical signatures of coordination were preferred by independent improvisers and naive listeners, who gave higher quality ratings to coupled interactions despite being blind to condition. We present these results and discuss their implications for music technology and JA research more generally.
WER we are and WER we think we are

Natural language processing of conversational speech requires the availability of high-quality transcripts. In this paper, we express our skepticism towards the recent reports of very low Word Error Rates (WERs) achieved by modern Automatic Speech Recognition (ASR) systems on benchmark datasets. We outline several problems with popular benchmarks and compare three state-of-the-art commercial ASR systems on an internal dataset of real-life spontaneous human conversations and HUB’05 public benchmark. We show that WERs are significantly higher than the best reported results. We formulate a set of guidelines which may aid in the creation of real-life, multi-domain datasets with high quality annotations for training and testing of robust ASR systems.