Miracle-dz/UniFAR-FTUs huggingface dataset:
Machine Learning-Based Detection of Open Source License Exceptions

From a legal perspective, software licenses govern the redistribution, reuse, and modification of software as both source and binary code. Free and Open Source Software (FOSS) licenses vary in the degree to which they are permissive or restrictive in allowing redistribution or modification under licenses different from the original one(s). In certain cases, developers may modify the license by appending to it an exception to specifically allow reuse or modification under a particular condition. These exceptions are an important factor to consider for license compliance analysis since they modify the standard (and widely understood) terms of the original license. In this work, we first perform a large-scale empirical study on the change history of over 51K FOSS systems aimed at quantitatively investigating the prevalence of known license exceptions and identifying new ones. Subsequently, we performed a study on the detection of license exceptions by relying on machine learning. We evaluated the license exception classification with four different supervised learners and sensitivity analysis. Finally, we present a categorization of license exceptions and explain their implications.
Immersion behavior of RF magnetron-assisted sputtered hydroxyapatite/titanium coatings in simulated body fluid.

The focus of the present study was on the dissolution/degradation behavior of a series of magnetron-sputtered, single-layered HA/Ti coatings on Ti-6Al-4V substrate immersed in SBF. Changes in coating morphology, crystal structure, and adhesion strength with immersion time are characterized. XRD, FTIR, and LVSEM results consistently indicate that highly crystalline monolithic HA coating is very dissolvable in SBF. The monolithic HA coating is largely delaminated in 3 weeks and entirely peeled off the substrate in 7 weeks. The dissolution is even greater for 95HA/5Ti coating, which severely disintegrated in only 1 week. The amorphous-like coatings sputtered from targets comprising 10 vol % or more Ti, however, appeared almost intact, and their adhesion strengths, which were all higher than 60 MPa, did not change much (within 10%) even after 14 weeks of immersion. The coatings from targets comprising roughly 10-50 vol % Ti combine advantages of high and nondeclining adhesion strength, high resistance to SBF attack, and possibly much higher bioactivity (with large amounts of Ca, P, etc., dissolved in the coatings) than that of Ti.
Matrix metalloproteinases 1 and 3, tissue inhibitor of metalloproteinase‐1 and the complex of metalloproteinase‐1/tissue inhibitor in plasma of patients with prostate cancer

We analyzed blood plasma concentrations of matrix metalloproteinase‐1 and ‐3 (MMP‐1; MMP‐3), the tissue inhibitor of metalloproteinase‐1 (TIMP‐1) and the complex MMP‐1/TIMP‐1, and looked for any correlation with prostate cancer stage. These components were measured by ELISA tests specific for these proteins in healthy male controls (n = 35), and in patients with benign prostatic hyperplasia (BPH; n = 29), with prostate cancer (PCa) without metastasis (T2,3pN0M0; n = 29) and with PCa with metastatic disease (T2,3,4pN1,2M1; n = 18). Mean values of MMP‐1 and of the complex MMP‐1/TIMP‐1 were not different among the 4 groups studied. The mean MMP‐3 and especially TIMP‐1 concentrations were significantly higher in PCa patients with metastases compared with controls, BPH and PCa patients without metastases. Ten of these 18 patients had TIMP‐1 concentrations higher than the upper reference limit. TIMP‐1 concentrations were correlated with staging but not with grading. Our results point towards plasma TIMP‐1 concentration as a potential marker of malignant progression of PCa. Int. J. Cancer 74:220‐223, 1997. © 1997 Wiley‐Liss, Inc.
Effects of (R)‐ and (S)‐isomers of β‐adrenergic agonists on eosinophil response to interleukin‐5

Background Racemic β2‐adrenergic receptor agonists (β2‐agonists) are used frequently to treat patients with asthma. Potential differences in the biological activities and clinical efficacies among racemic β2‐agonists and their isomers are controversial, and research into these possible differences is limited.
Selective Effects of Sodium Chlorate Treatment on the Sulfation of Heparan Sulfate*

We have analyzed the effect of sodium chlorate treatment of Madin-Darby canine kidney cells on the structure of heparan sulfate (HS), to assess how the various sulfation reactions during HS biosynthesis are affected by decreased availability of the sulfate donor 3′-phosphoadenosine 5′-phosphosulfate. Metabolically [3H]glucosamine-labeled HS was isolated from chlorate-treated and untreated Madin-Darby canine kidney cells and subjected to low pH nitrous acid cleavage. Saccharides representing (i) the N-sulfated domains, (ii) the domains of alternatingN-acetylated and N-sulfated disaccharide units, and (iii) the N-acetylated domains were recovered and subjected to compositional disaccharide analysis. Upon treatment with 50 mm chlorate, overall O-sulfation of HS was inhibited by ∼70%, whereas N-sulfation remained essentially unchanged. Low chlorate concentrations (5 or 20 mm) selectively reduced the 6-O-sulfation of HS, whereas treatment with 50 mm chlorate reduced both 2-O- and 6-O-sulfation. Analysis of saccharides representing the different domain types indicated that 6-O-sulfation was preferentially inhibited in the alternating domains. These data suggest that reduced 3′-phosphoadenosine 5′-phosphosulfate availability has distinct effects on the N- and O-sulfation of HS and thatO-sulfation is affected in a domain-specific fashion.
Short- and Intermediate-Term Angiographic and Clinical Outcomes of Patients with Various Grades of Coil Protrusions Following Embolization of Intracranial Aneurysms

After embolization, not uncommonly one sees coils protruding outside of the aneurysm into the lumen of the parent artery. What does this mean? The authors identified 256 patients with this finding from 3 different medical centers and set out to assess their short- and intermediate-term outcomes. They graded coil protrusions from a single loop projecting into less than half of the parent artery (grade 1) to those protruding into more than half (grade 3). Most protrusions in the series were grade 1. All patients were placed on aspirin and complications were not directly related to coil protrusions. The authors concluded that antiplatelet therapy is efficacious in preventing vessel thrombosis in this situation. BACKGROUND AND PURPOSE: An infrequent occurrence during endovascular treatment is protusion of detachable coils into the parent lumen with a subsequent thrombosis within in the parent vessel or embolic events. We report the short- and intermediate-term angiographic and clinical outcomes of patients who experience coil or loop protrusions and are managed with medical or additional endovascular treatments. MATERIALS AND METHODS: The coil protrusions were identified by retrospective review of 256 consecutive patients treated at 3 centers with endovascular embolizations for intracranial aneurysms and subsequently categorized as grade I when a single loop or coil protruded into the parent vessel lumen less than half the parent artery diameter; grades II and III were assigned when a single coil or loop protruded more than half the parent artery diameter, respectively. RESULTS: There were 19 patients with grade I (n = 9), grade II (n = 4), or grade III (n = 6) coil protrusions. Patients with active hemodynamic compromise (n = 6) had intracranial stents placed in addition to aspirin (indefinitely) and clopidogrel (range, 1–12 months; mean, 4.5 months) treatment. The remaining patients were placed on aspirin indefinitely. Complete aneurysm obliteration was achieved in all patients except in 3 in whom near-complete obliteration was achieved. Two patients had intraprocedural aneurysm ruptures, both of whom survived hospitalization. There were 4 deaths (4–21 days), all due to major strokes in different vascular distributions related to vasospasm (unrelated to the coil protrusion). CONCLUSIONS: Management of coil protrusions with antiplatelet therapy and placement of stents (in selected patients) appears efficacious in preventing vessel thrombosis.
Medroxyprogesterone acetate treatment reduces serum interleukin‐6 levels in patients with metastatic breast carcinoma

The serum interleukin (IL)‐6 concentration was very low in patients with metastatic breast carcinoma who had received oral medroxyprogesterone acetate (MPA) treatment as compared with those who had not. Accordingly, the authors conducted a prospective study to determine whether MPA treatment reduces the serum level of IL‐6 in patients with this disease.
Arabidopsis NAC transcription factor JUNGBRUNNEN1 affects thermomemory-associated genes and enhances heat stress tolerance in primed and unprimed conditions

We recently reported that the NAC transcription factor JUNGBRUNNEN1 (JUB1; ANAC042) extends longevity and increases tolerance to heat stress in Arabidopsis thaliana when overexpressed, while the opposite is observed in jub1-1 knock-down lines. Here we extend our previous findings by demonstrating that JUB1 also positively regulates plant survival under heat stress when plants were treated by a prior moderate (and non-lethal) temperature regime (so-called priming). We further find that JUB1 shows thermomemory-related expression, similar to two other genes previously reported to be important for thermopriming, i.e., HSFA2, encoding a heat shock factor, and HSA32, encoding a heat shock protein. Our analysis also identifies ASCORBATE PEROXIDASE2 (APX2) and the heat shock protein genes HSP18.2 and HSP21 as thermomemory-expressed genes, revealing them as new candidates for studies to decode the molecular processes controlling thermopriming.
Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI

Our approach to protein–protein docking includes three main steps. First we run PIPER, a new rigid body docking program. PIPER is based on the Fast Fourier Transform (FFT) correlation approach that has been extended to use pairwise interactions potentials, thereby substantially increasing the number of near‐native structures generated. The interaction potential is also new, based on the DARS (Decoys As the Reference State) principle. In the second step, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the conformations are refined by a new medium‐range optimization method SDU (Semi‐Definite programming based Underestimation). SDU has been developed to locate global minima within regions of the conformational space in which the energy function is funnel‐like. The method constructs a convex quadratic underestimator function based on a set of local energy minima, and uses this function to guide future sampling. The combined method performed reliably without the direct use of biological information in most CAPRI problems that did not require homology modeling, providing acceptable predictions for targets 21, and medium quality predictions for targets 25 and 26. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Sex and HIV serostatus differences in decision making under risk among substance-dependent individuals

ABSTRACT HIV+ individuals with and without substance use disorders make significantly poorer decisions when information about the probability and magnitude of wins and losses is not available. We administered the Game of Dice Task, a measure of decision making under risk that provides this information explicitly, to 92 HIV+ and 134 HIV– substance-dependent men and women. HIV+ participants made significantly poorer decisions than HIV– participants, but this deficit appeared more prominent among HIV+ women. These data indicate that decision making under risk is impaired among HIV+ substance-dependent individuals (SDIs). Potential factors for the HIV+ women’s relatively greater impairment are discussed.
Gender Differences in the Risk and Protective Factors Associated With PTSD: A Prospective Study of National Guard Troops Deployed to Iraq

This study examines gender differences in post-traumatic stress symptoms (PTSS) and PTSS risk/protective factors among soldiers deployed to Iraq. We pay special attention to two potentially modifiable military factors, military preparedness and unit cohesion, which may buffer the deleterious psychological effects of combat. Longitudinal data were collected on 922 New Jersey National Guard soldiers (91 women) deployed to Iraq in 2008. Anonymous surveys administered at pre- and post-deployment included the PTSD Checklist (PCL), the Unit Support Scale, and a preparedness scale adapted from the Iowa Gulf War Study. Bivariate analyses and hierarchical multiple regression were used to identify predictors of PTSS and their explanatory effects on the relationship between gender and PTSS. Women had a higher prevalence of probable post-deployment PTSD than men (18.7% vs. 8.7%; OR = 2.45; CI [1.37, 4.37]) and significantly higher post-deployment PTSS (33.73 vs. 27.37; p = .001). While there were no gender differences in combat exposure, women scored higher on pre-deployment PTSS (26.9 vs. 23.1; p ≤ .001) and lower on military preparedness (1.65 vs. 2.41; p ≤ .001) and unit cohesion (32.5 vs. 38.1; p ≤ .001). In a multivariate model, controlling for all PTSS risk/resilience factors reduced the gender difference as measured by the unstandardized Beta (B) by 45%, with 18% uniquely attributable to low cohesion and low preparedness. In the fully controlled model, gender remained a significant predictor of PTSS but the effect size was small (d = .26). Modifiable military institutional factors may account for much of the increased vulnerability of women soldiers to PTSD.
Risk and survival of cutaneous melanoma diagnosed subsequent to a previous cancer.

OBJECTIVE To understand the risk of cutaneous melanoma (CM) following a previous cancer. DESIGN Using the Surveillance, Epidemiology, and End Results database (1988-2007), we compared a cohort of patients diagnosed as having CM as a first cancer with a cohort of patients diagnosed as having CM following a previous cancer. PARTICIPANTS We included 70,819 patients with CM as a first primary cancer and 6353 patients with CM following a previous cancer. MAIN OUTCOME MEASURES We calculated the relative risk (RR) for development of primary CM following a previous cancer and used Cox modeling to examine survival characteristics of the 2 cohorts. RESULTS Patients younger than 45 years at first cancer diagnosis had significantly higher risk of CM following cutaneous melanoma (RR, 11.89; 95% CI, 10.83-13.03), other nonepithelial skin cancer (RR, 2.81; 95% CI, 1.13-5.79), Kaposi sarcoma (RR, 3.26; 95% CI 1.41-6.42), female breast cancer (RR, 1.38; (1.11-1.70), and lymphoma (RR, 1.79; (95% CI, 1.30-2.41). Patients 45 years or older at first cancer diagnosis had significantly higher risk of CM following cutaneous melanoma (RR, 8.36; 95% CI, 7.93-8.81), other nonepithelial skin cancer (RR, 2.00; 95% CI 1.35-2.86), ocular melanoma (RR, 5.34; 95% CI 3.42-7.94), female breast cancer (RR, 1.12; 95% CI, 1.03-1.21), prostate cancer (RR, 1.08; 95% CI, 1.03-1.13), thyroid cancer (RR, 1.40; 95% CI, 1.06-1.82), lymphoma (RR, 1.34; 95% CI, 1.16-1.55), and leukemia (RR, 1.79; 95% CI, 1.49-2.13). Characteristics associated with better survival in both cohorts included female sex, age younger than 45 years at melanoma diagnosis, being married, being white vs black, decreasing Breslow depth, lack of tumor ulceration, no nodal involvement, and absence of metastases. CONCLUSION Given that cutaneous melanoma is the most common second primary cancer in patients with a first CM (a risk that remains elevated for over 15 years), our results suggest the need for continued skin surveillance in melanoma survivors.
Development of a systems‐based in situ multiplex biomarker screening approach for the assessment of immunopathology and neural tissue plasticity in male rats after traumatic brain injury

Traumatic brain injuries (TBIs) pose a massive burden of disease and continue to be a leading cause of morbidity and mortality throughout the world. A major obstacle in developing effective treatments is the lack of comprehensive understanding of the underlying mechanisms that mediate tissue damage and recovery after TBI. As such, our work aims to highlight the development of a novel experimental platform capable of fully characterizing the underlying pathobiology that unfolds after TBI. This platform encompasses an empirically optimized multiplex immunohistochemistry staining and imaging system customized to screen for a myriad of biomarkers required to comprehensively evaluate the extent of neuroinflammation, neural tissue damage, and repair in response to TBI. Herein, we demonstrate that our multiplex biomarker screening platform is capable of evaluating changes in both the topographical location and functional states of resident and infiltrating cell types that play a role in neuropathology after controlled cortical impact injury to the brain in male Sprague–Dawley rats. Our results demonstrate that our multiplex biomarker screening platform lays the groundwork for the comprehensive characterization of changes that occur within the brain after TBI. Such work may ultimately lead to the understanding of the governing pathobiology of TBI, thereby fostering the development of novel therapeutic interventions tailored to produce optimal tissue protection, repair, and/or regeneration with minimal side effects, and may ultimately find utility in a wide variety of other neurological injuries, diseases, and disorders that share components of TBI pathobiology.
High-yield synthesis of amido-functionalized polyoctahedral oligomeric silsesquioxanes by using acyl chlorides.

Homosubstituted amido-functionalized polyoctahedral oligomeric silsesquioxanes (POSS) have been synthesized by using acyl chlorides in high yields (ca. 95%). The method proved to be superior over "conventional" syntheses applying carboxylic acids or acid anhydrides, which are much less efficient (ca. 60% yield). A palette of aryl and alkyl groups has been used as side-chains. The structures of the resulting amide-POSS are supported by multinuclear (1)H, (13)C, (29)Si NMR and FTIR spectroscopy and their full conversion into octasubstituted derivatives was confirmed using mass spectrometry. We also demonstrate that the functionalized silsesquioxanes with bulky organic side-chains attached to cubic siloxane core form spherical-like, well-separated nanoparticles with a size of approximately 5 nm.
Gene expression profiles of hepatic cell-type specific marker genes in progression of liver fibrosis.

AIM To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis. METHODS Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells), and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells. RESULTS The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSC-specific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis, suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocyte-specific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis. CONCLUSION Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibrogenesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis.
MPTP-induced vulnerability of dopamine neurons in A53T α-synuclein overexpressed mice with the potential involvement of DJ-1 downregulation

Familial Parkinson's disease (PD) has been linked to point mutations and duplication of the α-synuclein (α-syn) gene. Mutant α-syn expression increases the vulnerability of neurons to exogenous insults. In this study, we developed a new PD model in the transgenic mice expressing mutant hemizygous (hemi) or homozygous (homo) A53T α-synuclein (α-syn Tg) and their wildtype (WT) littermates by treatment with sub-toxic (10 mg/kg, i.p., daily for 5 days) or toxic (30 mg/kg, i.p., daily for 5 days) dose of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Tyrosine hydroxylase and Bcl-2 levels were reduced in the α-syn Tg but not WT mice by sub-toxic MPTP injection. In the adhesive removal test, time to remove paper was significantly increased only in the homo α-syn Tg mice. In the challenging beam test, the hemi and homo α-syn Tg mice spent significantly longer time to traverse as compared to that of WT group. In order to find out responsible proteins related with vulnerability of mutant α-syn expressed neurons, DJ-1 and ubiquitin enzyme expressions were examined. In the SN, DJ-1 and ubiquitin conjugating enzyme, UBE2N, levels were significantly decreased in the α-syn Tg mice. Moreover, A53T α-syn overexpression decreased DJ-1 expression in SH-SY5Y cells. These findings suggest that the vulnerability to oxidative injury such as MPTP of A53T α-syn mice can be explained by downregulation of DJ-1.
Comparison of the Enzymatic and Functional Properties of Three Cytosolic Carboxypeptidase Family Members*

Background: All cytosolic carboxypeptidase (CCP) family members catalyze deglutamylation of tubulin. Results: Nna1 (CCP1), CCP4, and CCP6 exhibit distinct sequence preferences and kinetics for synthetic polyglutamate substrates. CCP4 and CCP6 fail to rescue Purkinje cell degeneration in Nna1-dysfunctional mice. Conclusion: CCPs are not biologically equivalent in Purkinje neurons. Significance: The results expand the range of substrates and biological processes influenced by CCPs. Nna1 (CCP1) defines a subfamily of M14 metallocarboxypeptidases (CCP1–6) and is mutated in pcd (Purkinje cell degeneration) mice. Nna1, CCP4, and CCP6 are involved in the post-translational process of polyglutamylation, where they catalyze the removal of polyglutamate side chains. However, it is unknown whether these three cytosolic carboxypeptidases share identical enzymatic properties and redundant biological functions. We show that like Nna1, purified recombinant CCP4 and CCP6 deglutamylate tubulin, but unlike Nna1, neither rescues Purkinje cell degeneration in pcd mice, indicating that they do not have identical functions. Using biotin-based synthetic substrates, we established that the three enzymes are distinguishable based upon individual preferences for glutamate chain length, the amino acid immediately adjacent to the glutamate chain, and whether their activity is enhanced by nearby acidic amino acids. Nna1 and CCP4 remove the C-terminal glutamate from substrates with two or more glutamates, whereas CCP6 requires four or more glutamates. CCP4 behaves as a promiscuous glutamase, with little preference for chain length or neighboring amino acid composition. Besides glutamate chain length dependence, Nna1 and CCP6 exhibit higher kcat/Km when substrates contain nearby acidic amino acids. All cytosolic carboxypeptidases exhibit a monoglutamase activity when aspartic acid precedes a single glutamate, which, together with their other individual preferences for flanking amino acids, greatly increases the potential substrates for these enzymes and the biological processes in which they act. Additionally, Nna1 metabolized substrates mimicking the C terminus of tubulin in a way suggesting that the tyrosinated form of tubulin will accumulate in pcd mice.