Miracle-dz/UniFAR-FTUs huggingface dataset:
Similarity of plant functional traits and aggregation pattern in a subtropical forest

Abstract The distribution of species and communities in relation to environmental heterogeneity is a central focus in ecology. Co‐occurrence of species with similar functional traits is an indication that communities are determined in part by environmental filters. However, few studies have been designed to test how functional traits are selectively filtered by environmental conditions at local scales. Exploring the relationship between soil characteristics and plant traits is a step toward understanding the filtering hypothesis in determining plant distribution at local scale. Toward this end, we mapped all individual trees (diameter >1 cm) in a one‐ha subtropical forest of China in 2007 and 2015. We measured topographic and detailed soil properties within the field site, as well as plant leaf functional traits and demographic rates of the seven most common tree species. A second one‐ha study plot was established in 2015, to test and validate the general patterns that were drawn from first plot. We found that variation in species distribution at local scale can be explained by soil heterogeneity and plant functional traits. (From first plot). (1) Species dominant in habitats with high soil ammonium nitrogen and total phosphorus tended to have high specific leaf area (SLA) and relative growth rate (RGR). (2) Species dominant in low‐fertility habitats tended to have high leaf dry matter content (LDMC), ratio of chlorophyll a and b (ratioab), and leaf thickness (LT). The hypothesis that functional traits are selected in part by environmental filters and determine plant distribution at local scale was confirmed by the data of the first plot and a second regional site showed similar species distribution patterns.
Impact of MDM2 single nucleotide polymorphism on tumor onset in head and neck squamous cell carcinoma

Conclusions. The GG genotype of MDM2 SNP309 is associated with an earlier onset of head and neck squamous cell carcinoma (HNSCC) in the Japanese population. SNP309 may be a key factor in the tumorigenesis of HNSCC as well as other hereditary or sporadic tumors. Objective. This study was designed to evaluate the association between the single nucleotide polymorphism (SNP) 309 in the MDM2 gene with HNSCC. An MDM2 protein down-regulates the p53 pathway. Recently, an important SNP was discovered in the MDM2 promoter region, which could affect the tumorigenesis of HNSCC by attenuation of the p53 pathway. Patients and methods. Patients with 103 HNSCCs were genotyped using direct sequencing and real-time PCR. The relationship between the SNP309 genotypes and the clinicopathological features was statistically analyzed. Results. The number of patients genotyped to TT, TG, and GG was 29 (28%), 46 (44.7%), and 28 (27.2%), respectively. The average age at tumor onset was 65.6 years for TT, 62.9 years for TG, and 56.7 years for GG. The patients with the GG genotype had a significantly earlier tumor onset in comparison to those with the TT genotype (p=0.032).
Working With No Data: Semitic and Egyptian Studies Presented to Thomas O. Lambdin

Preface Tributes: John Huehnergard, Richard J. Clifford The Different Traditions of Mishnaic Hebrew - Moshe Bar-Asher Linguistics and Philology in the Study of Ancient Near Eastern Languages - Walter R. Bodine Mot Invites Baal to a Feast: Observations on a Difficult Ugaritic Text (CTA 5.i = KTU The Oldest Phoenician Inscription from Sardinia: The Fragmentary Stele from Nora - Frank Moore Cross Supralinear and in Palestinian Pointed Manuscripts of Hebrew and Aramaic from the Cairo Geniza - Steven E. Fassberg The Targumic Renderings of the Verb l histah wot: A Targumic Translation Convention - David M. Golomb Dialect Distributions in Canaan and the Deir Alla Inscriptions - Baruch Halpern Malahat al-qasd - Andras Hamori The Apocalypse of Hannah: Targum Jonathan of 1 Samuel 2:1-10 - Daniel J. Harrington The Divergence of the Egyptian Suffix Conjugation - Carleton T. Hodge The Cartonnage Case of Pa-di-mut, Harvard Semitic Museum 2230 - Susan T. Hollis Three Notes on Akkadian Morphology - John Huehnergard The Oldest Ethiopic Manuscript (K-9) of the Book of Enoch and Recent Studies of the Aramaic Fragments of Qumran Cave 4 - Ephraim Isaac Join the Apiru or Become One? - William L. Moran A Problem of Gemination in the Ethiopic Verbal System - H. Lee Perkins Some Observations on the Sibilants in the Second Millennium B.C. - Lamia R. Shehadeh The Textual Base for the Ethiopic Translation of 1 Enoch - James C. VanderKam Bibliography of the Writings of Thomas O. Lambdin
A phase 1/2A Trial of STA 5326, an oral interleukin‐12/23 inhibitor, in patients with active moderate to severe Crohn's disease

Background: Intestinal inflammation associated with Crohn's disease is characterized by a type 1 helper T cell response and elevated levels of interleukin (IL)‐12. We report our clinical experience with a novel oral IL‐12/IL‐23 inhibitor (STA 5326) for the treatment of active Crohn's disease. Materials and Methods: We conducted an open‐label, dose‐escalating trial of the orally delivered small molecule immunomodulator STA 5326 in 73 patients with active Crohn's disease (Crohn's disease activity index [CDAI] 220‐450, inclusive). Five cohorts of patients were treated for up to 4 weeks with 14 mg twice a day (bid), 35 mg daily (qd), 28 mg bid, 35 mg bid, or 70 mg qd. The endpoints of the study included safety and improvement in clinical activity measured by the CDAI and the Crohn's disease endoscopic index of severity. Results: STA 5326 was well tolerated. Reported adverse events were similar across dose cohorts. The most common (>15%) drug‐related adverse events observed were dizziness, nausea, headache, and fatigue. Clinical activity at day 28/29 was observed at qd doses of 28 mg and above for the clinical endpoints of response and remission: 70 points or greater decrease in CDAI (range 42%‐82% of patients); 100 points or greater decrease in CDAI (range 38%−64% of patients), and CDAI <150 (range 15%−36%). Conclusions: Oral qd dosing of STA 5326 for 4 weeks was well tolerated in doses up to 70 mg qd in patients with active moderate to severe Crohn's disease. Clinical activity was observed at qd doses of 28 mg and above.
The DNA methylation status of genes encoding Matrix metalloproteinases and tissue inhibitors of Matrix metalloproteinases in endometriosis

Endometriosis is a benign disease, with malignant properties. A necessary step in the progression of endometriosis is tissue remodeling, which is coordinated by the activities of matrix metalloproteinases (MMPs) and tissue inhibitors of matrix metalloproteinases (TIMPs). This study evaluated the regulation of abnormal MMP and TIMP gene expression during endometriosis. Among the two genes families, promoter regions of MMP2, MMP3, MMP7, TIMP3, and TIMP4 were significantly altered in proliferative‐phase endometriotic lesions compared to menstrual cycle‐matched eutopic tissue from endometriosis‐free women. In addition, a negative correlation was found between the DNA methylation status of the promoter region and transcript abundance of MMP2. Our findings suggest that changes in DNA methylation at the promoter region of MMP2 could underlie the changes in its expression in the ectopic endometria from patients with endometriosis.
HIV-1 chemokine coreceptor utilization in paired cerebrospinal fluid and plasma samples: a survey of subjects with viremia.

BACKGROUND Chemokine receptors serve as coreceptors for human immunodeficiency virus type 1 (HIV-1) entry, influence cell tropism, and may critically determine central nervous system infection pathogenesis. Using an in vitro functional entry assay, we examined utilization of 2 principal coreceptors in cerebrospinal fluid (CSF) and plasma in 46 subjects. METHODS Paired CSF and plasma samples were selected from subjects with a range of CD4 T cell counts. Amplified populations of env sequences were characterized as using CCR5 (R5), CXCR4 (X4), or both receptors (R5+X4). Individual clones derived from 3 subjects were analyzed for viral tropism and phylogeny. RESULTS CSF and plasma pairs were mainly concordant for R5 (36/46) or R5+X4 (5/46) viruses. However, 5 pairs were discordant, 2 of which had the R5+X4 phenotype in CSF despite having the R5 phenotype in plasma. Although R5+X4 tropism was associated with advanced immunodeficiency, all 4 subjects with acquired immunodeficiency syndrome dementia complex had R5 tropism in CSF. Clones derived from R5+X4-tropic populations revealed mixtures of R5 and X4 viruses and viruses able to utilize either coreceptor, suggesting both virus exchange between compartments and autonomous CSF virus evolution. CONCLUSIONS Although R5 viruses predominate in the CSF, HIV-1 populations able to utilize CXCR4 are also present. Discordant tropism in CSF and plasma may have implications for R5 inhibitor therapy.
Pseudomonas aeruginosa–Induced Inflammation in the Rat Extended-Wear Contact Lens Model

Purpose. To examine the early host response to Pseudomonas aeruginosa challenge in the extended contact lens–wearing rat model. Methods. Lewis rats were fitted with extended-wear lotrafilcon A hydrogel lenses in the left eye, and the right eye served as the control. Bacterial challenge was initiated in the experimental eye by fitting a bacteria-soaked contact lens and by topical delivery of the bacteria. On first detection of corneal opacity, slitlamp examination, histopathologic examination, viable bacteria counts, enzyme-linked immunosorbent assay, myeloperoxidase, Langerhans cell detection, and multiprobe ribonuclease protection assays were used to evaluate the early corneal response. Results. Analysis of bacterially challenged contact lens–wearing versus control rats showed Langerhans cells and polymorphonuclear neutrophils only in the experimentally challenged cornea. In addition, in the experimentally challenged cornea, ribonuclease protection and enzyme-linked immunosorbent analyses showed an upregulation of proinflammatory cytokines, including interleukins 1&bgr; and 6, suggesting that with contact lens wear, these cytokines contribute to the early corneal response and, potentially, disease. Conclusions. The contact lens–wearing rat model allows a unique analysis of the early effects of bacterial challenge in extended-wear contact lenses in the absence of corneal scarring, used in most rodent models. The rat model should be valuable to delineate further the effects of contact lens wear, including the testing of additional contact lens–related complications.
Characterization of elderly patients in rehabilitation: stroke versus hip fracture.

PURPOSE To compare the characteristics of elderly patients hospitalized for rehabilitation following stroke with those following hip fracture (HF). METHODS A prospective study in a geriatrics department of a general university hospital in southern Israel. Five hundred and sixteen hospitalized elderly patients were included in the study, 221 following stroke and 295 following HF. The characteristics were compared by univariate and logistic regression analyses. RESULTS The mean age (+/-SD) of the stroke patients was 71.7+/-7.8 years compared to 77.4+/-7.9 for HF (p < 0.000001). Fifty-three per cent of the stroke patients were women compared to 76% of the HF patients (p < 0.000001). Stroke patients had significantly lower levels of folic acid (p = 0.00002). HF patients had more hearing and visual impairments (p = 0.008 and p = 0.017, respectively), but these were related to age differences between the groups. The Folstein Minimental test result was significantly higher in the HF group (p = 0.002). There were no differences in the symptoms of depression score as measured by geriatric depression screening scale. The Functional Independent Measure scale showed a higher pre-event functional capacity among the stroke patients (p < 0.000001), but there was no difference in this scale on admission to rehabilitation or upon discharge. CONCLUSIONS There is a difference in the nature of the stroke and HF events. When either event involves an elderly patient with a broad range of limitations and diseases, a new medical condition develops. In this condition the symptoms of depression and the functional state at admission and upon discharge are not significantly different between these groups of patients.
A Review of Insider Threat Detection Approaches With IoT Perspective

Security professionals, government agencies, and corporate organizations have found an inherent need to prevent or mitigate attacks from insider threats. Accordingly, active research on insider threat detection has been conducted to prevent and mitigate adverse effects such as leakage of valuable information that may be caused by insiders. Along with the growth of Internet-of-Things (IoT), new security challenges arise in the existing security frameworks. Attack surfaces are significantly enlarged which could cause a severe risk in terms of company insider threat management. In this work, we provide a generalization of aspects of insider threats with IoT and analyze the surveyed literature based on both private and public sources. We then examine data sources considering IoT environments based on the characteristics and the structure of IoT (perceptual, network, and application layers). The result of reviewing the study shows that using the data source of the network and application layer is more suitable than the perceptual layer in the IoT environment. We also categorized each layer’s data sources according to their features, and we investigated research objectives and methods for each category. Finally, the potential for utilization and limitations under the IoT environment are presented at the end of each layer examination.
The Nuclear Import of TAF10 Is Regulated by One of Its Three Histone Fold Domain-Containing Interaction Partners

ABSTRACT TFIID, comprising the TATA box binding protein (TBP) and 13 TBP-associated factors (TAFs), plays a role in nucleation in the assembly of the RNA polymerase II preinitiation complexes on protein-encoding genes. TAFs are shared among other transcription regulatory complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC], STAGA, and PCAF/GCN5). Human TAF10, a subunit of both TFIID and TFTC, has three histone fold-containing interaction partners: TAF3, TAF8, and SPT7Like (SPT7L). In human cells, exogenously expressed TAF10 remains rather cytoplasmic and leptomycin B does not affect this localization. By using fluorescent fusion proteins, we show that TAF10 does not have an intrinsic nuclear localization signal (NLS) and needs one of its three interaction partners to be transported into the nucleus. When the NLS sequences of either TAF8 or SPT7L are mutated, TAF10 remains cytoplasmic, but a heterologous NLS can drive TAF10 into the nucleus. Experiments using fluorescence recovery after photobleaching show that TAF10 does not associate with any cytoplasmic partner but that once transported into the nucleus it binds to nuclear structures. TAF10 binding to importin β in vitro is dependent on the coexpression of either TAF8 or TAF3, but not SPT7L. The cytoplasmic-nuclear transport of TAF10 is naturally observed during the differentiation of adult male germ cells. Thus, here we describe a novel role of the three mammalian interacting partners in the nuclear localization of TAF10, and our data suggest that a complex network of regulated cytoplasmic associations may exist among these factors and that this network is important for the composition of different TFIID and TFTC-type complexes in the nucleus.
Simple prediction model for unfavorable outcome in ischemic stroke after intravenous thrombolytic therapy

ABSTRACT Objective We aimed to develop a model to predict unfavorable outcome in patients with acute ischemic stroke treated with intravenous thrombolytic therapy (IVT), based on simple variables present on admission. Methods Retrospective analysis of acute ischemic stroke patients treated with IVT in a hospital in Rio de Janeiro. Clinical and radiographic variables were selected for analysis. Multivariate logistic regression was used to develop a predictive model. Results We analyzed a total of 82 patients. Median National Institutes of Health Stroke Scale (NIHSS) on admission was 9 (3–22), 40.2% presented with a hyperdense artery sign (HAS), 62% had identifiable early parenchymal changes and 61.6% experienced a favorable outcome. An NIHSS score of > 12 on arrival, age > 70 and the presence of HAS were associated with the outcome, even after correction in a logistic regression model. Conclusion An NIHSS > 12 on arrival, presence of HAS and age > 70 years were predictors of unfavorable outcome at three months in patients with acute ischemic stroke treated with IVT.
Gene Expression Profiling in True Interval Breast Cancer Reveals Overactivation of the mTOR Signaling Pathway

Background: The development and progression of true interval breast cancers (tumors that truly appear after a negative screening mammogram) is known to be different from screen-detected cancers. However, the worse clinical behavior of true interval cancers is not fully understood from a biologic basis. We described the differential patterns of gene expression through microarray analysis in true interval and screen-detected cancers. Methods: An unsupervised exploratory gene expression profile analysis was performed on 10 samples (true interval cancers = 5; screen-detected cancers = 5) using Affymetrix Human Gene 1.0ST arrays and interpreted by Ingenuity Pathway Analysis. Differential expression of selected genes was confirmed in a validation series of 91 tumors (n = 12; n = 79) by immunohistochemistry and in 24 tumors (n = 8; n = 16) by reverse transcription quantitative PCR (RT-qPCR), in true interval and screen-detected cancers, respectively. Results: Exploratory gene expression analysis identified 1,060 differentially expressed genes (unadjusted P < 0.05) between study groups. On the basis of biologic implications, four genes were further validated: ceruloplasmin (CP) and ribosomal protein S6 kinase, 70 kDa, polypeptide 2 (RPS6KB2), both upregulated in true interval cancers; and phosphatase and tensin homolog (PTEN) and transforming growth factor beta receptor III (TGFBR3), downregulated in true interval cancers. Their differential expression was confirmed by RT-qPCR and immunohistochemistry, consistent with mTOR pathway overexpression in true interval cancers. Conclusions: True interval and screen-detected cancers show differential expression profile both at gene and protein levels. The mTOR signaling is significantly upregulated in true interval cancers, suggesting this pathway may mediate their aggressiveness. Impact: Linking epidemiologic factors and mTOR activation may be the basis for future personalized screening strategies in women at risk of true interval cancers. Cancer Epidemiol Biomarkers Prev; 23(2); 288–99. ©2013 AACR.
Conditional regulation of cyclooxygenase‐2 in tracheobronchial epithelial cells modulates pulmonary immunity

Cyclooxygenase‐2 (COX‐2) gene expression in the lung is induced in pathological conditions such as asthma and pneumonia; however, the exact impact of COX‐2 gene expression in the airway in regulating inflammatory and immunological response in the lung is not understood. To define a physiological role of inducible COX‐2 in airway epithelial cells, we developed a novel line of transgenic mice, referred to as CycloOxygenase‐2 TransActivated (COTA) mice, that overexpress a COX‐2 transgene in the distribution of the CC‐10 promoter in response to doxycycline. In response to doxycycline treatment, COX‐2 expression was increased in airway epithelium of COTA mice and whole lung tissue contained a three‐ to sevenfold increase in prostaglandin E2 (PGE2), prostaglandin D2 (PGD2) thromboxane B2 (TXB2) and 6‐Keto prostaglandin F2α (PGF2α) compared to wild‐type and untreated COTA mice. Interestingly, primary mouse tracheal epithelial cells from COTA mice produced only PGE2 by doxycycline‐induced COX‐2 activation, providing an indication of cellular specificity in terms of mediator production. In the ovalbumin model, in which doxycycline was given at the sensitization stage, there was an increase in interleukin (IL)‐4 level in lung tissue from COTA mice compared to untreated COTA and wild‐type mice. In addition, COTA mice that were treated with doxycycline had impaired clearance of Pseudomonas aeruginosa pneumonia compared to wild‐type mice. COX‐2 gene expression in airway epithelial cells has an important role in determining immunological response to infectious and allergic agents.
Effect of dialysis dose and membrane flux in maintenance hemodialysis.

BACKGROUND The effects of the dose of dialysis and the level of flux of the dialyzer membrane on mortality and morbidity among patients undergoing maintenance hemodialysis are uncertain. METHODS We undertook a randomized clinical trial in 1846 patients undergoing thrice-weekly dialysis, using a two-by-two factorial design to assign patients randomly to a standard or high dose of dialysis and to a low-flux or high-flux dialyzer. RESULTS In the standard-dose group, the mean (+/-SD) urea-reduction ratio was 66.3+/-2.5 percent, the single-pool Kt/V was 1.32+/-0.09, and the equilibrated Kt/V was 1.16+/-0.08; in the high-dose group, the values were 75.2+/-2.5 percent, 1.71+/-0.11, and 1.53+/-0.09, respectively. Flux, estimated on the basis of beta2-microglobulin clearance, was 3+/-7 ml per minute in the low-flux group and 34+/-11 ml per minute in the high-flux group. The primary outcome, death from any cause, was not significantly influenced by the dose or flux assignment: the relative risk of death in the high-dose group as compared with the standard-dose group was 0.96 (95 percent confidence interval, 0.84 to 1.10; P=0.53), and the relative risk of death in the high-flux group as compared with the low-flux group was 0.92 (95 percent confidence interval, 0.81 to 1.05; P=0.23). The main secondary outcomes (first hospitalization for cardiac causes or death from any cause, first hospitalization for infection or death from any cause, first 15 percent decrease in the serum albumin level or death from any cause, and all hospitalizations not related to vascular access) also did not differ significantly between either the dose groups or the flux groups. Possible benefits of the dose or flux interventions were suggested in two of seven prespecified subgroups of patients. CONCLUSIONS Patients undergoing hemodialysis thrice weekly appear to have no major benefit from a higher dialysis dose than that recommended by current U.S. guidelines or from the use of a high-flux membrane.
The Comparison and Interdependence of Maternal and Paternal Influences on Young Children's Behavior and Resilience

We investigated how mothers’ and fathers’ depressed mood and father–child and mother–child relationship predicted preschool children's problem behavior. The sample was 11,286 continuously intact, two-parent biological families of the United Kingdom's Millennium Cohort Study. We found that mother–child relationship and maternal depressed mood had larger effects on children's problem behavior than father–child relationship and paternal depressed mood. The effect of paternal depressed mood was completely mediated by quality of father–child relationship. There were significant moderator effects but only on internalizing problems. There was little evidence to suggest that, among children of this developmental stage, quality of father–child relationship buffers the effect of contextual risk (i.e., promotes resilience). Quality of mother–child relationship, in contrast, buffered the effect of socioeconomic disadvantage but only on emotional symptoms.