Miracle-dz/UniFAR-FTUs huggingface dataset:
Y‐box protein‐1 is a transcriptional regulator of BMP7

Bone morphogenetic protein‐7 (BMP7) is an endogenous antifibrogenic protein in the kidney which is down regulated in experimental chronic kidney diseases such as obstructive and diabetic nephropathy in parallel with progressively increasing TGFβ. In vitro studies were performed in Madin‐Darby Canine Kidney (MDCK)‐cells to identify transcriptional regulators of BMP7. Experiments with various BMP7 promoter fragments (465–4,267 bp) identify small proximal promoter segments that are transcriptionally activated by high glucose (3.2‐fold) but down regulated by TGFβ (0.2‐fold) compared to normal glucose. Protein binding to these DNA segments is increased by high glucose and decreased by TGFβ in a time‐dependent, progressive manner. Analysis of BMP7 promoter‐binding proteins with liquid chromatography/tandem mass spectrometry (LC/MS/MS) identifies seven unique, partially overlapping peptides, spanning 25% of the amino acid sequence of Y‐box protein‐1 (YB1). EMSA–Western blot combination experiments confirm that YB1 is a BMP7 promoter‐binding protein. YB1 knock‐down reduces transcriptional responses to high glucose and TGFβ by about one‐half, respectively. In addition, high glucose induces but TGFβ reduces nuclear translocation of YB1 from the cytoplasm. These studies identify YB1 as a transcriptional activator of BMP7 and helps to explain the progressive decline in renal BMP7 in diabetic nephropathy and other kidney diseases. J. Cell. Biochem. 112: 1130–1137, 2011. © 2011 Wiley‐Liss, Inc.
The Balance between Cell Division and Endoreplication Depends on E2FC-DPB, Transcription Factors Regulated by the Ubiquitin-SCFSKP2A Pathway in Arabidopsis[W]

The balance between cell proliferation, cell cycle arrest, and differentiation needed to maintain the organogenetic program depends on the coordination of gene expression, posttranslational modification, and specific proteolysis of cell cycle regulators. The G1/S and G2/M transitions are critical checkpoints controlled, in part, by cyclin-dependent kinases in the retinoblastoma (RBR)/E2F/DP pathway. Arabidopsis thaliana DPB is regulated by phosphorylation and targeted to proteasome-mediated proteolysis by the SCFSKP2A complex. In addition, DPB interacts in vivo with E2FC, because ectopic coexpression of E2FC and DPB produces severe developmental defects. To understand E2FC/DPB heterodimer function, we analyzed the effect of reducing E2FC mRNA levels with RNA interference. The e2fc-R plants developed organs with more but smaller cells and showed increased cell cycle marker gene expression and increased proliferative activity in developing leaves, meristems, and pericycle cells. This last feature produces plants with more lateral roots, consistent with an E2FC role in restricting lateral root initiation. The e2fc-R plants also show marked reductions in ploidy levels of mature leaves. These results indicate that the transition from cell division to the endocycle is sensitive to different pathways, E2FC/DPB being one of them. Our results show that E2FC/DPB is a key factor in controlling the balance between cell proliferation and the switch to the endocycle program.
Invited: Things, trouble, trust: On building trust in IoT systems

The emerging and much-touted Internet of Things (IoT) presents a variety of security and privacy challenges. Prominent among them is the establishment of trust in remote IoT devices, which is typically attained via remote attestation, a distinct security service that aims to ascertain the current state of a potentially compromised remote device. Remote attestation ranges from relatively heavy-weight secure hardware-based techniques, to light-weight software-based ones, and also includes approaches that blend software (e.g., control-flow integrity) and hardware features (e.g., PUFs). In this paper, we survey the landscape of state-of-the-art attestation techniques from the IoT device perspective and argue that most of them have a role to play in IoT trust establishment.
Online Learning of Eigenvectors

Computing the leading eigenvector of a symmetric real matrix is a fundamental primitive of numerical linear algebra with numerous applications. We consider a natural online extension of the leading eigenvector problem: a sequence of matrices is presented and the goal is to predict for each matrix a unit vector, with the overall goal of competing with the leading eigenvector of the cumulative matrix. Existing regret-minimization algorithms for this problem either require to compute an eigen decompostion every iteration, or suffer from a large dependency of the regret bound on the dimension. In both cases the algorithms are not practical for large scale applications. In this paper we present new algorithms that avoid both issues. On one hand they do not require any expensive matrix decompositions and on the other, they guarantee regret rates with a mild dependence on the dimension at most. In contrast to previous algorithms, our algorithms also admit implementations that enable to leverage sparsity in the data to further reduce computation. We extend our results to also handle non-symmetric matrices.
Body weight, gender and response to TNF-α blockers in axial spondyloarthritis.

OBJECTIVE The objective of this study was to determine whether BMI and gender could lead to a different response rate to anti-TNF agents in patients affected by axial SpA. METHODS One hundred and seventy patients with active axial SpA (defined as a BASDAI ≥ 4) treated with an anti-TNF agent [adalimumab (ADA), etanercept (ETA), infliximab (IFX)] were retrospectively evaluated. Patients were divided according to the baseline BMI as normal weight (BMI < 25), overweight (BMI 25-30) and obese (BMI ≥ 30). After 12 months of treatment a 50% improvement of the initial BASDAI (BASDAI50) was the primary end point and BASDAI ≤ 1 was the secondary end point. RESULTS After 12 months of anti-TNF treatment, 67.8% of men and 46.2% of women reached the BASDAI50 (P = 0.01). According to BMI categories, the rate of BASDAI50 achievement decreased from 72.8% in normal weight subjects to 54.5% in overweight and 30.4% in obese subjects (P < 0.001). In the logistic regression analysis, the best independent predictors of failure to obtain a BASDAI50 response at the 12th month of therapy in axial SpA patients were female gender [odds ratio (OR) 3.23 (95% CI 1.52, 7.14)] and a BMI ≥ 30 [OR 3.57 (95% CI 1.15, 11.11)]. Analysing outcomes based on IFX therapy (the larger subgroup), the BASDAI50 response rate fell from 79.0% in normal weight subjects to 56.7% in overweight and 16.7% in obese subjects (P < 0.001). No significant differences were observed with ADA and ETA. CONCLUSION Data suggest that being female, overweight and mostly obese is associated with a lower rate of success in obtaining response status in axial SpA patients treated with anti-TNF drugs. Body weight could represent a modifiable factor to reach the best outcome in axial SpA patients treated with TNF blockers.
Estimating double thumbnails for music recordings

Audio thumbnailing, which aims at finding the most representative audio segment of a music recording, is an important task in music information retrieval. In general, the notion of a thumbnail is not well-defined and several musical parts may be good thumbnail candidates. For example, for popular music, both a verse and a refrain section may serve as suitable thumbnail candidates. Instead of considering only one thumbnail, we consider in this paper the problem of finding the two most representative segments that correspond to different musical parts. We denote these two segments as double thumbnails. As our main technical contributions, we propose two approaches for computing double thumbnails, both extending a previously introduced repetition-based thumbnailing procedure. In the first approach, which is straightforward, we simply apply the original thumbnailing procedure two times in an iterative fashion. In the second approach, we introduce a novel method for jointly estimating the two thumbnails within one optimization procedure. Finally, we report on experimental results demonstrating the performances of the two double thumbnailing procedures and indicate directions towards full music structure analysis.
Integrating a Large, Monolingual Corpus as Translation Memory into Statistical Machine translation

Translation memories (TM) are widely used in the localization industry to improve consistency and speed of human translation. Several approaches have been presented to integrate the bilingual translation units of TMs into statistical machine translation (SMT). We present an extension of these approaches to the integration of partial matches found in a large, monolingual corpus in the target language, using cross-language information retrieval (CLIR) techniques. We use locality-sensitive hashing (LSH) for efficient coarse-grained retrieval of match candidates, which are then filtered by finegrained fuzzy matching, and finally used to re-rank the n-best SMT output. We show consistent and significant improvements over a state-of-the-art SMT system, across different domains and language pairs on tens of millions of sentences.
Improved Secure Efficient Delegated Private Set Intersection

Private Set Intersection (PSI) is a vital cryptographic technique used for securely computing common data of different sets. In PSI protocols, often two parties hope to find their common set elements without needing to disclose their uncommon ones. In recent years, the cloud has been playing an influential role in PSI protocols which often need huge computational tasks. In 2017, Abadi et al. introduced a scheme named EO-PSI which uses a cloud to pass on the main computations to it and does not include any public-key operations. In EO-PSI, parties need to set up secure channels beforehand; otherwise, an attacker can easily eavesdrop on communications between honest parties and find private information. This paper presents an improved EO-PSI scheme which has the edge on the previous scheme in terms of privacy and complexity. By providing possible attacks on the prior scheme, we show the necessity of using secure channels between parties. Also, our proposed protocol is secure against passive attacks without having to have any secure channels. We measure the protocol's overhead and show that computational complexity is considerably reduced and also is fairer compared to the previous scheme.
High-yield of memory elements from carbon nanotube field-effect transistors with atomic layer deposited gate dielectric

Carbon nanotube field-effect transistors (CNT FETs) have been proposed as possible building blocks for future nano-electronics. But a challenge with CNT FETs is that they appear to randomly display varying amounts of hysteresis in their transfer characteristics. The hysteresis is often attributed to charge trapping in the dielectric layer between the nanotube and the gate. We find that the memory effect can be controlled by carefully designing the gate dielectric in nm-thin layers. By using atomic layer depositions (ALD) of HfO2 and TiO2 in a triple-layer configuration, we achieve to our knowledge the first CNT FETs with consistent and narrowly distributed memory effects in their transfer characteristics. The study includes 94 CNT FET samples, providing a good basis for statistics on the hysteresis seen in five different CNT-gate configurations.
Bacillus anthracis Virulent Plasmid pX02 Genes Found in Large Plasmids of Two Other Bacillus Species

ABSTRACT In order to cause the disease anthrax, Bacillus anthracis requires two plasmids, pX01 and pX02, which carry toxin and capsule genes, respectively, that are used as genetic targets in the laboratory detection of the bacterium. Clinical, forensic, and environmental samples that test positive by PCR protocols established by the Centers for Disease Control and Prevention for B. anthracis are considered to be potentially B. anthracis until confirmed by culture and a secondary battery of tests. We report the presence of 10 genes (acpA, capA, capB, capC, capR, capD, IS1627, ORF 48, ORF 61, and repA) and the sequence for the capsule promoter normally found on pX02 in Bacillus circulans and a Bacillus species closely related to Bacillus luciferensis. Tests revealed these sequences to be present on a large plasmid in each isolate. The 11 sequences consistently matched to B. anthracis plasmid pX02, GenBank accession numbers AF188935.1, AE011191.1, and AE017335.3. The percent nucleotide identities for capD and the capsule promoter were 99.9% and 99.7%, respectively, and for the remaining nine genes, the nucleotide identity was 100% for both isolates. The presence of these genes, which are usually associated with the pX02 plasmid, in two soil Bacillus species unrelated to B. anthracis alerts us to the necessity of identifying additional sequences that will signal the presence of B. anthracis in clinical, forensic, and environmental samples.
Next-generation sequencing reveals phylogeographic structure Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences and a species tree for recent bird divergences

The multi-species coalescent provides an elegant theoretical frame-work for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a ﬁnite-sites model of mutation, eﬀectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 ampliﬁed fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).
KRas and BRaf mutational status analysis from formalin-fixed, paraffin-embedded tissues using multiplex polymerase chain reaction-based assay.

CONTEXT Monoclonal anti-epidermal growth factor receptor antibodies bind to the epidermal growth factor receptor and inhibit receptor kinase activity. Clinical trials have indicated that evaluation of the mutational status of KRas and BRaf is necessary to exclude patients who are resistant to the clinical benefit of anti-epidermal growth factor receptor therapy. OBJECTIVE To develop a multiplex polymerase chain reaction-based assay for the evaluation of KRas and BRaf mutational status. DESIGN A sample-saving and cost-effective, multiplex polymerase chain reaction-based assay to detect somatic mutations in KRAS exon 2 and exon 3 as well as in BRAF exon 15 was developed. The same primer pairs could be successfully used in amplification of a single DNA fragment under the same conditions. RESULTS DNA isolated from 20 retrospective formalin-fixed, paraffin-embedded samples of colorectal cancer was screened for mutations using the multiplex polymerase chain reaction assay followed by dideoxy-termination sequencing. Five samples bearing mutations-p.G12D (identified twice), p.G12V, p.G12S, and p.G13D, all encoded in KRAS exon 2-were identified. Three samples were found bearing amino acid substitution p.V600E of BRaf. The detected KRas and BRaf mutations were found to be mutually exclusive. CONCLUSIONS A multiplex polymerase chain reaction-based amplification followed by dideoxy-termination sequencing may be used advantageously for the evaluation of KRas and BRaf mutational status from formalin-fixed, paraffin-embedded samples.
Influence of Restorative Materials on Color of Implant-Supported Single Crowns in Esthetic Zone: A Spectrophotometric Evaluation

Restorations of 98 implant-supported single crowns in anterior maxillary area were divided into 5 groups: zirconia abutment, titanium abutment, and gold/gold hue abutment with zirconia coping, respectively, and titanium abutment with metal coping as well as gold/gold hue abutment with metal coping. A reflectance spectrophotometer was used to evaluate the color difference between the implant crowns and contralateral/neighboring teeth, as well as the color difference between the peri-implant soft tissue and the natural marginal mucosa. The mucosal discoloration score was used for subjective evaluation of the esthetic outcome of soft tissue around implant-supported single crowns in the anterior zone, and the crown color match score was used for subjective evaluation of the esthetic outcome of implant-supported restoration. ANOVA analysis was used to compare the differences among groups and Spearman correlation was used to test the relationships. A gold/gold hue abutment with zirconia coping was the best choice for an esthetic crown and the all-ceramic combination was the best for peri-implant soft tissue. Significant correlation was found between the spectrophotometric color difference of peri-implant soft tissue and mucosal discoloration score, while no significant correlation was found between the total spectrophotometric color difference of implant crown and crown color match score.
Mutations in XPB and XPD helicases found in xeroderma pigmentosum patients impair the transcription function of TFIIH

As part of TFIIH, XPB and XPD helicases have been shown to play a role in nucleotide excision repair (NER). Mutations in these subunits are associated with three genetic disorders: xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD). The strong heterogeneous clinical features observed in these patients cannot be explained by defects in NER alone. We decided to look at the transcriptional activity of TFIIH from cell lines of XP individuals. We set up an immunopurification procedure to isolate purified TFIIH from patient cell extracts. We demonstrated that mutations in two XP‐B/CS patients decrease the transcriptional activity of the corresponding TFIIH by preventing promoter opening. The defect of XPB in transcription can be circumvented by artificial opening of the promoter. Western blot analysis and enzymatic assays indicate that XPD mutations affect the stoichiometric composition of TFIIH due to a weakness in the interaction between XPD–CAK complex and the core TFIIH, resulting in a partial reduction of transcription activity. This work, in addition to clarifying the role of the various TFIIH subunits, supports the current hypothesis that XP‐B/D patients are more likely to suffer from transcription repair syndromes rather than DNA repair disorders alone.
Coping with phonological variation in early lexical acquisition

Mapping word forms onto their corresponding meanings is one of the most complex tasks that young infants acquiring their native language have to perform. This is due to the fact that an utterance can refer to many different aspects of a scene, a problem known as referential ambiguity (Quine 1960). An even more basic problem, though, is that it is not easy to find word forms to start with. In fact, the speech waveform is continuous, and word boundaries are not readily available. Moreover, words often surface with different phonetic forms due to the application of postlexical phonological processes; that is, surface word forms exhibit what we call phonological variation. Most models of lexical acquisition assume that infants can somehow extract unique word forms out of the speech stream before they acquire the meaning of words (e.g. Siskind 1996). Hence, they propose a solution to the problem of referential ambiguity, thereby assuming that the problems of finding word boundaries and undoing phonological variation have already been solved. There is evidence that infants can indeed find word boundaries before they have a lexicon (Jusczyk & Aslin 1995). By contrast, virtually nothing is known concerning the question of how prelexical infants deal with phonological variation. In this paper, we will examine if and how infants that do not have a lexicon might undo phonological variation, i.e. deduce which phonological processes apply and infer unique underlying word forms that will constitute lexical entries. The various intricacies of phonological variation for lexical acquisition can be illustrated within a single language, i.e. Korean. First, consider the allophonic rule of obstruent voicing. This rule voices plain obstruents that occur between two voiced segments, as illustrated in (1); voiced obstruents do not otherwise occur in Korean.
Data Collection and Analysis

The focus of this chapter is on methods of data collection and analysis for the assessment of learning processes and complex performance, the last part of the empirical cycle after theory development and experimental design. In the introduction (van Gog and Paas), the general background and the relation between the chapter sections are briefly described. The section by Savenye, Robinson, Niemczyk, and Atkinson focuses on methods of data collection and analysis for assessment of individual learning processes, whereas the section by Johnson and O’Connor is concerned with methods for assessment of group learning processes. The chapter section by van Gog, Rikers, and Ayres discusses the assessment of complex performance, and the final chapter section by Duley, Ward, Szalma, and Hancock is concerned with setting up laboratories to measure learning and complex performance.
Partially Common-Semantic Pursuit for RGB-D Object Recognition

For the RGB-D object recognition task, the robust and rich representations can boost the performance. Most works employ feature learning approaches to learn specific representation for the RGB and depth modalities independently, while some directly learn common property. Different from them, this paper proposes a novel supervised feature learning method for RGB-D object recognition, named Partially Common-Semantic Learning (PCSL), which jointly captures the complementary and consistency semantic information from RGB and depth modalities. The complementary information is revealed by the individual modality, while the consistency is exploited by both modalities simultaneously. In PCSL, Reconstruction Independent Component Analysis (RICA) is extended to integrate the supervised information and learn both of the complementary and partially shared common semantic information. The proposed approach is evaluated on two public RGB-D datasets and achieves better performance than several state-of-the-art methods.
Extremely thin-body ballistic n-MOSFET designs involving transport in mixed Γ-L valleys

Transistor designs based on using mixed Γ-L valleys for electron transport are proposed to overcome the DOS bottleneck while maintaining high injection velocities. Using a self consistent top-of-the-barrier transport model, improved current density over Si is demonstrated in GaAs/AlAsSb, GaSb/AlAsSb and Ge-on-insulator (Ge-OI) based single-gate (SG) thin-body n-channel metal-oxide-semiconductor field-effect transistors (nMOSFETs). All the proposed designs successively begin to outperform strained-Si-on-insulator (sSi-OI) and InAs-on-insulator (InAs-OI) in terms of ON state currents as the effective oxide thickness (EOT) is reduced below 0.7 nm. InAs-OI still exhibits the lowest intrinsic delay (τ ) due to its single Γ valley.