Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear rotation-invariant coordinates for meshes

We introduce a rigid motion invariant mesh representation based on discrete forms defined on the mesh. The reconstruction of mesh geometry from this representation requires solving two sparse linear systems that arise from the discrete forms: the first system defines the relationship between local frames on the mesh, and the second encodes the position of the vertices via the local frames. The reconstructed geometry is unique up to a rigid transformation of the mesh. We define surface editing operations by placing user-defined constraints on the local frames and the vertex positions. These constraints are incorporated in the two linear reconstruction systems, and their solution produces a deformed surface geometry that preserves the local differential properties in the least-squares sense. Linear combination of shapes expressed with our representation enables linear shape interpolation that correctly handles rotations. We demonstrate the effectiveness of the new representation with various detail-preserving editing operators and shape morphing.
Gradual recruitment and selective clearing generate germ plasm aggregates in the zebrafish embryo

Determination of primordial germ cells (PGCs) is one of the earliest decisions in animal embryogenesis. In many species, PGCs are determined through maternally-inherited germ plasm ribonucleoparticles (RNPs). In zebrafish, these are transmitted during oogenesis as dispersed RNPs, which after fertilization multimerize and become recruited as large aggregates at furrows for the first and second cell cycles. Here, we show that the number of recruited germ plasm RNPs is halved every cell cycle. We also show that germ plasm RNPs are recruited during the third cell cycle, but only transiently. Our data support a mechanism in which systematic local gathering of germ plasm RNPs during cytokinesis and threshold-dependent clearing contribute to forming germ plasm aggregates with the highest RNP number and germ cell-inducing potential.
SemFuzz: Semantics-based Automatic Generation of Proof-of-Concept Exploits

Patches and related information about software vulnerabilities are often made available to the public, aiming to facilitate timely fixes. Unfortunately, the slow paces of system updates (30 days on average) often present to the attackers enough time to recover hidden bugs for attacking the unpatched systems. Making things worse is the potential to automatically generate exploits on input-validation flaws through reverse-engineering patches, even though such vulnerabilities are relatively rare (e.g., 5% among all Linux kernel vulnerabilities in last few years). Less understood, however, are the implications of other bug-related information (e.g., bug descriptions in CVE), particularly whether utilization of such information can facilitate exploit generation, even on other vulnerability types that have never been automatically attacked. In this paper, we seek to use such information to generate proof-of-concept (PoC) exploits for the vulnerability types never automatically attacked. Unlike an input validation flaw that is often patched by adding missing sanitization checks, fixing other vulnerability types is more complicated, usually involving replacement of the whole chunk of code. Without understanding of the code changed, automatic exploit becomes less likely. To address this challenge, we present SemFuzz, a novel technique leveraging vulnerability-related text (e.g., CVE reports and Linux git logs) to guide automatic generation of PoC exploits. Such an end-to-end approach is made possible by natural-language processing (NLP) based information extraction and a semantics-based fuzzing process guided by such information. Running over 112 Linux kernel flaws reported in the past five years, SemFuzz successfully triggered 18 of them, and further discovered one zero-day and one undisclosed vulnerabilities. These flaws include use-after-free, memory corruption, information leak, etc., indicating that more complicated flaws can also be automatically attacked. This finding calls into question the way vulnerability-related information is shared today.
A robust dynamic inversion technique for asymptotic tracking control of an aircraft

In this paper, a tracking controller is developed for an aircraft model subject to uncertainties in the dynamics and additive state-dependent nonlinear disturbance-like terms. In the design of the controller, dynamic inversion technique is utilized in conjunction with a robust term. Only the output of aircraft dynamics is utilized in the controller design and acceleration measurements are not required. Lyapunov based stability analysis is used to prove global asymptotic tracking.
Enhancing PV Penetration in LV Networks Using Reactive Power Control and On Load Tap Changer With Existing Transformers

Voltage rise beyond statuary limits in low voltage (LV) ac networks due to high photovoltaic (PV) penetration and its mitigation using multiple techniques was assessed. Investigations using a real rural domestic overhead LV network were done through load flow simulations. A three-phase four wire medium length LV network with a fixed tap transformer and PV inverters operating at unity power factor was able to host PV between 79%–98% of transformer ratings for five different PV configurations. For the case studied at this penetration level three, limiting factors (voltage, thermal loading limits of lines, and transformer) come together. Three techniques were utilized to control the voltage across the LV network. On load tap changer (OLTC) control was found more robust than reactive power control (RPC). Hybrid control (OLTC and RPC) was found beneficial only for extra high PV penetration scenarios. Replacement of a few critical line spans and the existing transformer with higher capacity conductors and an OLTC equipped transformer (higher size) enabled the network to host an additional 50%–90% PV. The unequal distribution of single-phase PV systems among three phases has negative effects on penetration. Consideration of PV integration while planning new LV networks and retrofitting of OLTCs with existing transformers, could make the LV system more PV friendly. The RPC option, though less effective than OLTC due to increased current, can be beneficial at medium penetrations where OLTC may become a costly solution.
Late-onset systemic lupus erythematosus in Latin Americans: a distinct subgroup?

Objective To examine the characteristics of patients who developed late onset systemic lupus erythematosus (SLE) in the GLADEL (Grupo Latino Americano de Estudio del Lupus) cohort of patients with SLE. Methods Patients with SLE of less than two years of disease duration, seen at 34 centers of nine Latin American countries, were included. Late-onset was defined as >50 years of age at time of first SLE-related symptom. Clinical and laboratory manifestations, activity index (SLEDAI), and damage index (SLICC/ACR- DI) were ascertained at time of entry and during the course (cumulative incidence). Features were compared between the two patient groups (<50 and ≥50) using descriptive statistics and hypothesis tests. Logistic regression was performed to examine the association of late-onset lupus, adjusting for other variables. Results Of the 1480 patients included, 102 patients (6.9 %) had late-onset SLE, 87% of which were female. Patients with late-onset SLE had a shorter follow-up (3.6 vs. 4.4 years, p < 0.002) and a longer time to diagnosis (10.1 vs. 5.8 months, p < 0.001) compared to the younger onset group. Malar rash, photosensitivity, and renal involvement were less prevalent while interstitial lung disease, pleural effusions, and sicca symptoms were more frequent in the older age group (p > 0.05). In multivariable analysis, late onset was independently associated with higher odds of ocular (OR = 3.66, 95% CI = 2.15–6.23), pulmonary (OR = 2.04, 95% CI = 1.01–4.11), and cardiovascular (OR = 1.76, 95% CI = 1.04–2.98) involvement and lower odds of cutaneous involvement (OR = 0.41, 95% CI = 0.21–0.80), number of cumulative SLE criteria (OR = 0.79, 95% CI = 0.64–0.97), use of cyclophosphamide (OR = 0.47, 95% CI = 0.24–0.95), and anti-RNP antibodies (OR = 0.43, 95% CI = 0.20–0.91). A Cox regression model revealed a higher risk of dying in older onset than the younger-onset SLE (OR = 2.61, 95% CI = 1.2–5.6). Conclusion Late-onset SLE in Latin Americans had a distinct disease expression compared to the younger-onset group. The disease seems to be mild with lower cumulative SLE criteria, reduced renal/mucocutaneous involvements, and less use of cyclophosphamide. Nevertheless, these patients have a higher risk of death and of ocular, pulmonary, and cardiovascular involvements.
A Viral RNA Structural Element Alters Host Recognition of Nonself RNA

Alphaviruses use secondary structural elements in their genomic RNA to avoid host detection. Although interferon (IFN) signaling induces genes that limit viral infection, many pathogenic viruses overcome this host response. As an example, 2'-O methylation of the 5′ cap of viral RNA subverts mammalian antiviral responses by evading restriction of Ifit1, an IFN-stimulated gene that regulates protein synthesis. However, alphaviruses replicate efficiently in cells expressing Ifit1 even though their genomic RNA has a 5′ cap lacking 2'-O methylation. We show that pathogenic alphaviruses use secondary structural motifs within the 5′ untranslated region (UTR) of their RNA to alter Ifit1 binding and function. Mutations within the 5′-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. These results identify an evasion mechanism by which viruses use RNA structural motifs to avoid immune restriction. Keeping Alphaviruses Under Wraps Viruses mutate to avoid detection, and the host responds in kind. For example, 2′-O methylation of the 5′ cap of viral RNA allows viruses to escape detection by the interferon-stimulated host defense protein, IFIT1. Alphaviruses, however, lack this modification but are able to remain undetected in the presence of IFIT1. How? Using a combination of viral mutants and biochemical analysis, Hyde et al. (p. 783, published online 30 January) found that alphaviruses contain secondary structural motifs in the 5′ untranslated region of their genomic RNA that allow them to avoid detection by IFIT1. When these regions were rendered nonfunctional, IFIT1 was able to keep the virus under control.
Cyclotron resonance of the magnetic ratchet effect and second harmonic generation in bilayer graphene

We model the magnetic ratchet effect in bilayer graphene in which a dc electric current is produced by an ac electric field of frequency $\omega$ in the presence of a steady in-plane magnetic field and inversion-symmetry breaking. In bilayer graphene, the ratchet effect is tunable by an external metallic gate which breaks inversion symmetry. For a tilted magnetic field, the perpendicular field component induces cyclotron motion with frequency $\omega_c$ and we find that the dc current displays cyclotron resonance at $\omega_c = \omega$, although this peak in the current is actually smaller than its value at $\omega_c = 0$. Second harmonic generation, however, is greatly enhanced by resonances at $\omega_c = \omega$ and $\omega_c = 2\omega$ for which the current is generally much larger than at $\omega_c = 0$.
International Prognostic Score in advanced-stage Hodgkin's lymphoma: altered utility in the modern era.

PURPOSE The International Prognostic Score (IPS) is the most widely used risk stratification index for Hodgkin's lymphoma (HL). It is based on patients treated before 1992 and predicts 5-year freedom from progression (FFP) and overall survival (OS) ranging from 42% to 84% and 56% to 89%, respectively. The IPS has not been validated in a recently treated population in which outcomes have improved compared with historic results. PATIENTS AND METHODS By using the British Columbia Cancer Agency Lymphoid Cancer Database, we identified all patients age ≥ 16 years newly diagnosed with advanced-stage HL (stage III to IV, or stage I to II with "B" symptoms or bulky disease ≥ 10 cm) from 1980 to 2010, treated with curative intent with doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) or an ABVD-equivalent regimen with complete clinical information. RESULTS In all, 740 patients were identified. Five-year FFP and OS were 78% and 90%, respectively. The IPS was prognostic for both FFP (P < .001) and OS (P < .001), with 5-year FFP ranging from 62% to 88% and 5-year OS ranging from 67% to 98%. Analysis limited to patients age 16 to 65 years (n = 686) demonstrated a narrower range of outcomes, with 5-year FFP ranging from 70% to 88% and 5-year OS ranging from 73% to 98%. CONCLUSION The IPS remains prognostic for advanced-stage HL, but the range of outcomes has narrowed considerably. This improvement in outcome with ABVD should be acknowledged before consideration of alternate initial therapies and when comparing results from current trials with those of historic controls.
Measuring factor IX activity of nonacog beta pegol with commercially available one‐stage clotting and chromogenic assay kits: a two‐center study

Essentials Validated assays are required to precisely measure factor IX (FIX) activity in FIX products. N9‐GP and two other FIX products were assessed in various coagulation assay systems at two sites. Large variations in FIX activity measurements were observed for N9‐GP using some assays. One‐stage and chromogenic assays accurately measuring FIX activity for N9‐GP were identified.
Possible involvement of the M2 anti‐inflammatory macrophage phenotype in growth of human gliomas

Within tumours, many non‐neoplastic cells such as fibroblasts, endothelial cells, and macrophages assist tumour growth by producing various growth factors and pro‐angiogenic cytokines. Various tumour‐derived molecules drive tumour‐associated macrophages towards an anti‐inflammatory phenotype (M2) and thus promoting tumour growth. Here we investigated microglia/macrophage differentiation in glioma tissues by means of immunostaining of paraffin‐embedded glioma samples. The number of microglia/macrophages with positive staining for CD163 and CD204, which are believed to be markers for M2 macrophages, was correlated with the histological grade of the gliomas. The ratio of M2 macrophages in the tumour‐associated microglia/macrophages was also associated with the histological grade. Culture supernatant from the glioma cell line can stimulate macrophages to develop into the M2 phenotype in vitro. Macrophage colony‐stimulating factor (M‐CSF), which strongly induces M2 polarization of macrophages, was significantly correlated with histological malignancy and with the proportion of M2 microglia/macrophages in vivo. In addition, the proportion of M2 microglia/macrophages and M‐CSF expression in tumour cells correlated well with proliferation of glioblastoma cells. These results suggest that tumour‐derived M‐CSF induces a shift of microglia/macrophages towards the M2 phenotype, which influences tumour growth. Evaluation of the proportion of M2 microglia/macrophages and M‐CSF expression in tumour tissue would be useful for assessment of microglia/macrophage proliferative activity and the prognosis of patients with gliomas. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Hu Antigen R (HuR) Functions as an Alternative Pre-mRNA Splicing Regulator of Fas Apoptosis-promoting Receptor on Exon Definition*

Exclusion of exon 6 by alternative RNA splicing of the primary transcript of the apoptosis receptor Fas produces a soluble isoform that prevents programmed cell death. I report that antiapoptotic regulator Hu antigen R (HuR, ELAVL1), a member of the embryonic lethal, abnormal vision, Drosophila-like (ELAVL) family, promotes Fas exon 6 skipping by binding to an exonic splicing silencer. HuR inhibits the association of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor 65 kDa (U2AF65) with the upstream 3′ splice site, without decreasing recognition of the downstream 5′ splice site by U1 snRNP but by antagonizing the role of TIA-1 (T-cell intracellular antigen 1)/TIAR (TIA-1 related protein) on exon definition. Remarkably, U1 snRNP-mediated recognition of the 5′ splice site is partially required for efficient U2AF65 inhibition. Further, the silencing capacity of HuR as splicing regulator resides in the RRM1 and hinge-RRM3 domains. Taken together, these results support a functional link between HuR as repressor of alternative Fas splicing and the molecular mechanisms modulating programmed cell death.
Genetics of second-generation antipsychotic and mood stabilizer-induced weight gain in bipolar disorder: common and specific effects of key regulators of fat-mass homoeostasis genes

Objective Second-generation antipsychotics (SGAP) and mood stabilizers (MS) are prescribed widely for the treatment of bipolar disorder, but they are associated with the risk of relevant side-effects, among which is weight gain. The identification of genes that predispose to weight gain would represent a useful tool to evaluate the risk–benefit ratio of treatment. Materials and methods This study investigated the genetic factors associated with weight gain in bipolar patients treated with SGAP, MS and their combinations (n=486). Single-nucleotide polymorphisms belonging to 16 candidate genes supported by the literature were investigated in the Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD) genome-wide dataset. Linear regression models were constructed including age, sex, initial weight and prescription of SGAP at high risk for inducing weight gain (olanzapine or clozapine) as covariates. Genes harbouring single-nucleotide polymorphisms associated with phenotypes were investigated by a pathway analysis. Results No association was found between phenotypes and individual polymorphisms or pathways after multiple-test correction. HTR2C, LEP, FTO and TBC1D1 represented the top genes for weight gain during treatment with a SGAP and/or MS. A genome-wide signal (FTO rs9930506) associated previously with obesity was associated with psychotropic-induced weight gain. The genes that influenced both SGAP and MS weight gain were FTO, TBC1D1, MTHFR and HRH1. ADCY9, ADCY5 and PRKAG2 were interesting candidate genes that emerged from the pathway analysis. Conclusion This study was the first to compare the genes involved in SGAP-induced and MS-induced weight gain. Individual genes probably play a limited role in psychotropic-induced weight gain; further studies should focus on the extension from known candidate genes to wider groups of molecular pathways.
Analysis of facial expressiveness during experimentally induced heat pain

To develop automatic pain monitoring systems, we need a deep understanding of pain expression and its influencing factors and we need datasets with high-quality labels. This work analyzes the variation of facial activity with pain stimulus intensity and among subjects. We propose two distinct methods to assess facial expressiveness and apply them on the BioVid Heat Pain Database. Experimental results show that facial response is rare during low intensity pain stimulation and that the proposed measures can successfully identify highly expressive individuals, for whom pain stimuli can be classified reliably, and non-expressive individuals, who may have felt less pain than intended and encoded in labels.
NanoPCR observation: different levels of DNA replication fidelity in nanoparticle-enhanced polymerase chain reactions

Nanoparticle-assisted PCR (polymerase chain reaction) technology is getting more and more attention recently. It is believed that some of the DNA recombinant technologies will be upgraded by nanotechnology in the near future, among which DNA replication is one of the core manipulation techniques. So whether or not the DNA replication fidelity is compromised in nanoparticle-assisted PCR is a question. In this study, a total of 16 different metallic and non-metallic nanoparticles (NPs) were tested for their effects on DNA replication fidelity in vitro and in vivo. Sixteen types of nanomaterials were distinctly different in enhancing the PCR efficiency, and their relative capacity to retain DNA replication fidelity was largely different from each other based on rpsL gene mutation assay. Generally speaking, metallic nanoparticles induced larger error rates in DNA replication fidelity than non-metallic nanoparticles, and non-metallic nanomaterials such as carbon nanopowder or nanotubes were still safe as PCR enhancers because they did not compromise the DNA replication fidelity in the Taq DNA polymerase-based PCR system.
A novel family of tyrosine integrases encoded by the temperate pleolipovirus SNJ2

Abstract Genomes of halophilic archaea typically contain multiple loci of integrated mobile genetic elements (MGEs). Despite the abundance of these elements, however, mechanisms underlying their site-specific integration and excision have not been investigated. Here, we identified and characterized a novel recombination system encoded by the temperate pleolipovirus SNJ2, which infects haloarchaeon Natrinema sp. J7-1. SNJ2 genome is inserted into the tRNAMet gene and flanked by 14 bp direct repeats corresponding to attachment core sites. We showed that SNJ2 encodes an integrase (IntSNJ2) that excises the proviral genome from its host cell chromosome, but requires two small accessory proteins, Orf2 and Orf3, for integration. These proteins were co-transcribed with IntSNJ2 to form an operon. Homology searches showed that IntSNJ2-type integrases are widespread in haloarchaeal genomes and are associated with various integrated MGEs. Importantly, we confirmed that SNJ2-like recombination systems are encoded by haloarchaea from three different genera and are critical for integration and excision. Finally, phylogenetic analysis suggested that IntSNJ2-type recombinases belong to a novel family of archaeal integrases distinct from previously characterized recombinases, including those from the archaeal SSV- and pNOB8-type families.
Modifying behavioral phenotypes in Fmr1KO mice: genetic background differences reveal autistic‐like responses

Fragile X syndrome (FXS) is the most common inherited form of intellectual disability in humans. In addition to cognitive impairment, patients may exhibit hyperactivity, attention deficits, social difficulties and anxiety, and autistic‐like behaviors. The degree to which patients display these behaviors varies considerably and is influenced by family history, suggesting that genetic modifiers play a role in the expression of behaviors in FXS. Several studies have examined behavior in a mouse model of FXS in which the Fmr1 gene has been ablated. Most of those studies were done in Fmr1 knockout mice on a pure C57BL/6 or FVB strain background. To gain a better understanding of the effects of genetic background on behaviors resulting from the loss of Fmr1 gene expression, we generated F1 hybrid lines from female Fmr1 heterozygous mice on a pure C57BL/6J background bred with male Fmr1 wild‐type (WT) mice of various background strains (A/J, DBA/2J, FVB/NJ, 129S1/SvImJ and CD‐1). Male Fmr1 knockout and WT littermates from each line were examined in an extensive behavioral test battery. Results clearly indicate that multiple behavioral responses are dependent on genetic background, including autistic‐like traits that are present on limited genetic backgrounds. This approach has allowed us to identify improved models for different behavioral symptoms present in FXS including autistic‐like traits.