Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Identity Problem for the Special Linear Group and the Heisenberg Group

We study the identity problem for matrices, i.e., whether the identity matrix is in a semigroup generated by a given set of generators. In particular we consider the identity problem for the special linear group following recent NP-completeness result for ${\rm SL}(2,\mathbb{Z})$ and the undecidability for ${\rm SL}(4,\mathbb{Z})$ generated by $48$ matrices. First we show that there is no embedding from pairs of words into $3\times3$ integer matrices with determinant one, i.e., into ${\rm SL}(3,\mathbb{Z})$ extending previously known result that there is no embedding into $\mathbb{C}^{2\times 2}$. Apart from theoretical importance of the result it can be seen as a strong evidence that the computational problems in \slthreez are decidable. The result excludes the most natural possibility of encoding the Post correspondence problem into ${\rm SL}(3,\mathbb{Z})$, where the matrix products extended by the right multiplication correspond to the Turing machine simulation. Then we show that the identity problem is decidable in polynomial time for an important subgroup of ${\rm SL}(3,\mathbb{Z})$, the Heisenberg group ${\rm H}(3,\mathbb{Z})$. Furthermore, we extend the decidability result for ${\rm H}(n,\mathbb{Q})$ in any dimension $n$. Finally we are tightening the gap on decidability question for this long standing open problem by improving the undecidability result for the identity problem in ${\rm SL}(4,\mathbb{Z})$ substantially reducing the bound on the size of the generator set from $48$ to $8$ by developing a novel reduction technique.
Paranoia and post-traumatic stress disorder in the months after a physical assault: a longitudinal study examining shared and differential predictors

Background Being physically assaulted is known to increase the risk of the occurrence of post-traumatic stress disorder (PTSD) symptoms but it may also skew judgements about the intentions of other people. The objectives of the study were to assess paranoia and PTSD after an assault and to test whether theory-derived cognitive factors predicted the persistence of these problems. Method At 4 weeks after hospital attendance due to an assault, 106 people were assessed on multiple symptom measures (including virtual reality) and cognitive factors from models of paranoia and PTSD. The symptom measures were repeated 3 and 6 months later. Results Factor analysis indicated that paranoia and PTSD were distinct experiences, though positively correlated. At 4 weeks, 33% of participants met diagnostic criteria for PTSD, falling to 16% at follow-up. Of the group at the first assessment, 80% reported that since the assault they were excessively fearful of other people, which over time fell to 66%. Almost all the cognitive factors (including information-processing style during the trauma, mental defeat, qualities of unwanted memories, self-blame, negative thoughts about self, worry, safety behaviours, anomalous internal experiences and cognitive inflexibility) predicted later paranoia and PTSD, but there was little evidence of differential prediction. Conclusions Paranoia after an assault may be common and distinguishable from PTSD but predicted by a strikingly similar range of factors.
Pharmacokinetic profile of Ceftiofur Hydrochloride Injection in lactating Holstein dairy cows

Ceftiofur (CEF), a broad-spectrum third-generation cephalosporin, exhibits a good activity against a broad range of gram-negative and gram-positive bacteria, including many that produce β-lactamase. To design a rational dosage regimen for the drug in lactating Holstein dairy cows, the pharmacokinetic properties of ceftiofur hydrochloride injection were investigated in six cows after intravenous, intramuscular, and subcutaneous administration of single dose of 2.2 mg/kg BW (body weight). Plasma concentration-time curves and relevant parameters were best described by noncompartmental analysis through WinNonlin 6.3 software. After subcutaneous administration, the absolute bioavailability was 61.12% and the T1/2λz (elimination half-life) was 8.67 ± 0.72 hr. The Cmax (maximum plasma concentration) was 0.88 ± 0.21 μg/ml and Tmax (the time after initial injection to when Cmax occurs) was 1.50 ± 0.55 hr. The MRT (mean residence time) was 11.00 ± 0.30 hr. Following intramuscular administration, the Cmax (1.09 ± 0.21 μg/ml) was achieved at Tmax (1.20 ± 0.26 hr) with an absolute availability of 70.52%. In this study, the detailed pharmacokinetic profiles of free and total CEF showed that this drug is widely distributed and rapidly eliminated and may contribute to a better understanding of the usage of ceftiofur hydrochloride injection in Holstein dairy cows.
Structural Recurrent Neural Network (SRNN) for Group Activity Analysis

A group of persons can be analyzed at various semantic levels such as individual actions, their interactions, and the activity of the entire group. In this paper, we propose a structural recurrent neural network (SRNN) that uses a series of interconnected RNNs to jointly capture the actions of individuals, their interactions, as well as the group activity. While previous structural recurrent neural networks assumed that the number of nodes and edges is constant, we use a grid pooling layer to address the fact that the number of individuals in a group can vary. We evaluate two variants of the structural recurrent neural network on the Volleyball Dataset.
Sumoylation of Turnip mosaic virus RNA Polymerase Promotes Viral Infection by Counteracting the Host NPR1-Mediated Immune Response

Sumoylation of the RNA-dependent RNA polymerase from Turnip mosaic virus by SUMO3 suppresses host immunity and alters the subcellular localization of this polymerase to promote viral infection. Sumoylation is a transient, reversible dynamic posttranslational modification that regulates diverse cellular processes including plant-pathogen interactions. Sumoylation of NPR1, a master regulator of basal and systemic acquired resistance to a broad spectrum of plant pathogens, activates the defense response. Here, we report that NIb, the only RNA-dependent RNA polymerase of Turnip mosaic virus (TuMV) that targets the nucleus upon translation, interacts exclusively with and is sumoylated by SUMO3 (SMALL UBIQUITIN-LIKE MODIFIER3), but not the three other Arabidopsis thaliana SUMO paralogs. TuMV infection upregulates SUMO3 expression, and the sumoylation of NIb by SUMO3 regulates the nuclear-cytoplasmic partitioning of NIb. We identified the SUMO-interacting motif in NIb that is essential for its sumoylation and found that knockout or overexpression of SUMO3 suppresses TuMV replication and attenuates viral symptoms, suggesting that SUMO3 plays dual roles as a host factor of TuMV and as an antiviral defender. Sumoylation of NIb by SUMO3 is crucial for its role in suppressing the host immune response. Taken together, our findings reveal that sumoylation of NIb promotes TuMV infection by retargeting NIb from the nucleus to the cytoplasm where viral replication takes place and by suppressing host antiviral responses through counteracting the TuMV infection-induced, SUMO3-activated, NPR1-mediated resistance pathway.
Hypoxia upregulates HIG2 expression and contributes to bevacizumab resistance in glioblastoma

Hypoxia contributes to the maintenance of stem-like cells in glioblastoma (GBM), and activates vascular mimicry and tumor resistance to anti-angiogenesis treatments. The present study examined the expression patterns and biological significance of hypoxia-inducible protein 2 (HIG2, also known as HILPDA) in GBM. HIG2 was highly expressed in gliomas and was correlated with tumor grade, and high HIG2 expression independently predicted poor GBM patient prognosis. HIG2 was upregulated during hypoxia and by hypoxia mimics, and HIG2 knockdown in GBM cells inhibited cell proliferation and invasion. HIF1α bound to the HIG2 promoter and increased its expression in GBM cells, and HIG2 upregulated HIF1α expression. Reconstruction of a HIG2-related molecular network using bioinformatics methods revealed that HIG2 is closely correlated with angiogenesis genes, such as VEGFA, in GBM. HIG2 levels positively correlated with VEGFA in GBM samples. In addition, treatment of transplanted xenograft nude mice with bevacizumab (anti-angiogenesis therapy) resulted in HIG2 upregulation at late stages. We conclude that HIG2 is overexpressed in GBM and upregulated by hypoxia, and is a potential novel therapeutic target. HIG2 overexpression is an independent prognostic indicator and may promote tumor resistance to anti-angiogenesis treatments.
Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks

The diverse, specialized genes present in today’s lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and alterations in one gene may drive reciprocal changes in its proteins’ binding partners. Like many complex networks, these gene regulatory networks (GRNs) are composed of communities, or clusters of genes with relatively high connectivity. A deep understanding of the relationship between the evolutionary history of single genes and the topological properties of the underlying GRN is integral to evolutionary genetics. Here, we show that the topological properties of an acute myeloid leukemia GRN and a general human GRN are strongly coupled with its genes’ evolutionary properties. Slowly evolving (“cold”), old genes tend to interact with each other, as do rapidly evolving (“hot”), young genes. This naturally causes genes to segregate into community structures with relatively homogeneous evolutionary histories. We argue that gene duplication placed old, cold genes and communities at the center of the networks, and young, hot genes and communities at the periphery. We demonstrate this with single-node centrality measures and two new measures of efficiency, the set efficiency and the interset efficiency. We conclude that these methods for studying the relationships between a GRN’s community structures and its genes’ evolutionary properties provide new perspectives for understanding evolutionary genetics.
Protecting Sensory Data against Sensitive Inferences

There is growing concern about how personal data are used when users grant applications direct access to the sensors of their mobile devices. In fact, high resolution temporal data generated by motion sensors reflect directly the activities of a user and indirectly physical and demographic attributes. In this paper, we propose a feature learning architecture for mobile devices that provides flexible and negotiable privacy-preserving sensor data transmission by appropriately transforming raw sensor data. The objective is to move from the current binary setting of granting or not permission to an application, toward a model that allows users to grant each application permission over a limited range of inferences according to the provided services. The internal structure of each component of the proposed architecture can be flexibly changed and the trade-off between privacy and utility can be negotiated between the constraints of the user and the underlying application. We validated the proposed architecture in an activity recognition application using two real-world datasets, with the objective of recognizing an activity without disclosing gender as an example of private information. Results show that the proposed framework maintains the usefulness of the transformed data for activity recognition, with an average loss of only around three percentage points, while reducing the possibility of gender classification to around 50%, the target random guess, from more than 90% when using raw sensor data. We also present and distribute MotionSense, a new dataset for activity and attribute recognition collected from motion sensors.
Association of Morning Hypertension Subtype With Vascular Target Organ Damage and Central Hemodynamics

Background A recent study reported that morning hypertension is associated with poor cardiovascular outcomes in hypertensive patients. However, it is unclear whether morning hypertension associated with sustained nocturnal hypertension and that associated with morning blood pressure (BP) surge differ in terms of their effects on cardiovascular target organ damage and clinical outcomes. The present study aimed to determine the association of morning hypertension with/without nocturnal hypertension with vascular target organ damage and central hemodynamics in patients at high risk for cardiovascular disease. Methods and Results Ambulatory BP monitoring was performed and central BP was measured in 1070 consecutive patients with high cardiovascular risk. We grouped morning hypertension into the following 3 subtypes: (I) morning normotension; (II) morning hypertension without nocturnal hypertension; and (III) morning hypertension with nocturnal hypertension. Morning hypertension was noted in 469 (43.8%) patients and morning hypertension with nocturnal hypertension was noted in 374 (34.9%) patients. The central systolic/diastolic BP and carotid to femoral pulse wave velocity were significantly higher in the subtype III group than in the subtype I and II groups (all P<0.001). Subtype III (versus subtype I) was an independent predictor of central hypertension and high‐risk arterial stiffness (P<0.001 and P=0.018, respectively) but not vascular damage in a fully adjusted model (model Y). Conclusions Morning hypertension, especially that associated with nocturnal hypertension, is related to high central BP and increased arterial stiffness. Further studies on whether morning hypertension with or without nocturnal hypertension is related to clinical outcomes should be performed. Clinical Trial Registration URL: http://www.clinicaltrials. gov. Unique identifier: NCT02003781.
Memory Contextualization: The Role of Prefrontal Cortex in Functional Integration across Item and Context Representational Regions

Abstract Memory recall is facilitated when retrieval occurs in the original encoding context. This context dependency effect likely results from the automatic binding of central elements of an experience with contextual features (i.e., memory “contextualization”) during encoding. However, despite a vast body of research investigating the neural correlates of explicit associative memory, the neural interactions during encoding that predict implicit context-dependent memory remain unknown. Twenty-six participants underwent fMRI during encoding of salient stimuli (faces), which were overlaid onto unique background images (contexts). To index subsequent context-dependent memory, face recognition was tested either in intact or rearranged contexts, after scanning. Enhanced face recognition in intact relative to rearranged contexts evidenced successful memory contextualization. Overall subsequent memory effects (brain activity predicting whether items were later remembered vs. forgotten) were found in the left inferior frontal gyrus (IFG) and right amygdala. Effective connectivity analyses showed that stronger context-dependent memory was associated with stronger coupling of the left IFG with face- and place-responsive areas, both within and between participants. Our findings indicate an important role for the IFG in integrating information across widespread regions involved in the representation of salient items and contextual features.
Theory Rate-Limiting Steps in Yeast Protein Translation

Premal Shah,1 Yang Ding,1 Malwina Niemczyk,2,3 Grzegorz Kudla,2,4 and Joshua B. Plotkin1,* 1Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA 2Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH3 9LP, UK 3Present address: Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK 4Present address: Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK *Correspondence: jplotkin@sas.upenn. edu http://dx.doi. org/10.1016/j.cell. 2013.05. 049
Antigen-binding cells in the cecal tonsil and Peyer's patches of the chicken after bovine serum albumin administration.

It has been previously reported in the chicken that the ellipsoid-associated cells (EAC), which are considered to be a type of splenic dendritic cell, migrate from the spleen into the blood after binding antigen on their surface. In the current study we traced the localization of these cells within two peripheral lymphoid organs, the cecal tonsil (CT) and the Peyer's patches (PP). The migration of the cells was followed by light microscopy using bovine serum albumin bound to biotin and conjugated to gold particles as a histochemically identifiable antigen detected as peroxidase reaction. The observations showed that the EAC after entering the circulating blood migrated into the lymphoid tissue of the CT and the PP. As a consequence, the antigen-binding cells were found in the diffuse lymphoid tissue and the germinal centers in both lymphoid organs. In the former location they were seen 24 h after the second antigen administration and in the germinal centers on Day 3. In addition, antigen-binding cells started to be observed in the lymphoid tissue at the same time as T and B cells were found to proliferate by using 5-bromo-2'-deoxyuridine. Based upon these findings, we suggested that the EAC have a role as antigen-transporting cells from the spleen to the CT and the PP via the blood stream. Furthermore, our results provided evidence that after the antigen-transporting EAC entered the above-mentioned organs, these cells behaved as antigen-presenting cells in both the T- and B-dependent areas. (ABSTRACT TRUNCATED AT 250 WORDS)
The transmission of aflatoxin B1 into eggs.

Abstract Aflatoxin B1 was incorporated at levels of 0.1, 0.2, and 0.4 p.p.m. in a laying mash ration which was fed to laying hens. The eggs from hens at all three feeding levels contained measurable amounts of aflatoxin B1. Some eggs from hens given the ration containing 0.4 p.p.m. were stored at 3° C. for 9 months before analysis; no aflatoxin was found in these eggs.
Radiofrequency ablation (RFA) vs. argon plasma coagulation (APC) for the management of gastric antral vascular ectasia (GAVE) in patients with and without cirrhosis: results from a retrospective analysis of a large cohort of patients treated at a single center

Abstract Introduction and study aims Gastric antral vascular ectasia (GAVE) is a mucosal abnormality associated with multiple conditions, most notably cirrhosis and systemic sclerosis, that causes indolent gastrointestinal bleeding. It is primarily managed with endoscopic therapy. Traditionally, GAVE is endoscopically ablated using argon plasma coagulation (APC) but radiofrequency ablation (RFA) is emerging as an alternative modality. No prior comparison of the 2 modalities has been published. We retrospectively compared the effects of GAVE ablation with either RFA, APC or both in the largest cohort of patients thus far presented. We also attempt to discern what effect concomitant cirrhosis has on response to treatment. Patients and methods After receiving IRB approval, we reviewed our electronic health records to identify all patients who underwent endoscopic evaluation for GAVE between January, 2011 and October, 2016. We compared important variables between APC and RFA, as well as between cirrhosis and non-cirrhosis, using the Chi-square test and the Wilcoxon two-sample test as appropriate. Results During our study period, 81 patients were endoscopically evaluated for GAVE. 24 patients were treated with APC alone, 28 with RFA alone and 25 patients received both treatment modalities. APC-treated patients underwent a mean of 2.4 treatment sessions with a mean of 205 days between treatments. RFA-treated patients underwent a mean of 2.3 treatment sessions with a mean of 100 days between treatments. Hemoglobin values remained stable or increased in all patients during our study period and there were no significant differences in Hgb trend between those treated with APC and those with RFA. Conclusions RFA and APC were both effective in treating bleeding from GAVE. Though we found subtle differences, patients underwent a similar number of treatment sessions and had similar procedure times and a similar time between sessions no matter the treatment modality used.
Disabled‐1 dorsal horn spinal cord neurons co‐express Lmx1b and function in nociceptive circuits

The Reelin‐signaling pathway is essential for correct neuronal positioning within the central nervous system. Mutant mice with a deletion of Reelin, its lipoprotein receptors, or its intracellular adaptor protein Disabled‐1 (Dab1), exhibit nociceptive abnormalities: thermal (heat) hyperalgesia and reduced mechanical sensitivity. To determine dorsal horn alterations associated with these nociceptive abnormalities, we first characterized the correctly positioned Dab1 neurons in wild‐type and mispositioned neurons in Reelin‐signaling pathway mutant lumbar spinal cord. Using immunofluorescence, we found that 70% of the numerous Dab1 neurons in Reln+/+ laminae I–II and 67% of those in the lateral reticulated area and lateral spinal nucleus (LSN) co‐express the LIM‐homeobox transcription factor 1 beta (Lmx1b), an excitatory glutamatergic neuron marker. Evidence of Dab1‐ and Dab1‐Lmx1b neuronal positioning errors was found within the isolectin B4 terminal region of Reln−/− lamina IIinner and in the lateral reticulated area and LSN, where about 50% of the Dab1‐Lmx1b neurons are missing. Importantly, Dab1‐Lmx1b neurons in laminae I–II and the lateral reticulated area express Fos after noxious thermal or mechanical stimulation and thus participate in these circuits. In another pain relevant locus – the lateral cervical nucleus (LCN), we also found about a 50% loss of Dab1‐Lmx1b neurons in Reln−/− mice. We suggest that extensively mispositioned Dab1 projection neurons in the lateral reticulated area, LSN, and LCN and the more subtle positioning errors of Dab1 interneurons in laminae I–II contribute to the abnormalities in pain responses found in Reelin‐signaling pathway mutants.
Pelvic Morphology in Homo erectus and Early Homo

The evolution of the hominin pelvis is generally seen as involving two broad stages: the establishment of bipedal pelvic morphology by the mid‐Pliocene (or earlier), followed by architectural changes necessary to enlarge the birth canal in response to increased encephalization in Pleistocene members of the genus Homo. Pelvic and proximal femoral morphology in early Homo (namely H. erectus) has been seen as transitional between these stages, reflecting structural changes necessitated by greater body size (and perhaps moderate increases in brain size) overlain upon a basically primitive pelvic architecture. Here we review the history of thought on the evolution of the pelvis in early Homo, as well as recent fossil discoveries that have improved our understanding of diversity in pelvic morphology in early Homo and late australopiths. These discoveries (1) suggest that the “femoropelvic complex” characteristic of H. erectus emerged after the divergence of various lineages of early Homo (that is, it is not plesiomorphic for the genus) and (2) raise questions about the role that evolutionary change in brain size in the genus Homo played in the emergence of derived features seen in the pelvis of modern humans. Anat Rec, 300:964–977, 2017. © 2017 Wiley Periodicals, Inc.