Miracle-dz/UniFAR-FTUs huggingface dataset:
WHITEPAPER A primer on perfluoroalkyl substances ( PFAS ) – emerging contaminants in drinking water

Polyand perfluorinated substances (PFAS) are man-made chemicals used globally since the 1960s in a variety of industrial and commercial products. These compounds were designed to resist heat, oil, stains, grease, and water and have vastly improved the quality of modern life. The unique ability of PFAS to repel both oil and water has led to their principal application in stain repellant products (carpet, furniture/upholstery), nonstick cookware, waterproof clothing (e.g., Gortex, Tyvek) and coated paper. In addition, PFAS will produce a stable foam that can flow across liquid solvents, which has led to their widespread use as a high performance “aqueous film-forming foam” (AFFF). AFFF was used for firefighting burning fuels at military bases, airports, oil refineries, and firefighting training facilities.
Featured Article: Immunomodulatory effect of hemozoin on pneumocyte apoptosis via CARD9 pathway, a possibly retarding pulmonary resolution

Plasmodium falciparum, the most virulent malaria parasite species, causes severe symptoms especially acute lung injury (ALI), of which characterized by alveolar epithelium and endothelium destruction and accelerated to blood–gas-barrier breakdown. Parasitized erythrocytes, endothelial cells, monocytes, and cytokines are all involved in this mechanism, but hemozoin (HZ), the parasitic waste from heme detoxification, also mainly contributes. In addition, it is not clear why type II pneumocyte proliferation, alveolar restorative stage, is rare in malaria-associated ALI. To address this, in vitro culture of A549 cells with Plasmodium HZ or with interleukin (IL)-1β triggered by HZ and monocytes (HZ-IL-1β) was conducted to determine their alveolar apoptotic effect using ethidium bromide/acridine orange staining, annexin-V-FITC/propidium iodide staining, and electron mircroscopic study. Caspase recruitment domain-containing protein 9 (CARD9), the apoptotic regulator gene, and IL-1β were quantified by reverse-transcriptase PCR. Junctional cellular defects were characterized by immunohistochemical staining of E-cadherin. The results revealed that cellular apoptosis and CARD9 expression levels were extremely high 24 h after induction by HZ-IL-1β when compared to the HZ- and non-treated groups. E-cadherin was markedly down-regulated by HZ-IL-1β and HZ treatments. CARD9 expression was positively correlated with IL-1β expression and the number of apoptotic cells. Interestingly, the localization of HZ in the vesicular surfactant of apoptotic pneumocyte was also identified and submitted to be a cause of alveolar resolution abnormality. Thus, HZ triggers monocytes to produce IL-1β and induces pneumocyte type II apoptosis through CARD9 pathway in association with down-regulated E-cadherin, which probably impairs alveolar resolution in malaria-associated ALI. Impact statement The present work shows the physical and immunomodulatory properties of hemozoin on the induction of pneumocyte apoptosis in relation to IL-1β production through the CARD9 pathway. This occurrence may be a possible pathway for the retardation of lung resolution leading to blood–gas-barrier breakdown. Our findings lead to the understanding of the host–parasite relationship focusing on the dysfunction in ALI induced by HZ, a possible pathway of the recovering lung epithelial retardation in malaria-associated ARDS.
HYPOPHOSPHATEMIC RICKETS: CASE REPORT

ABSTRACT Objective: Early diagnosis and immediate treatment of hypophosphatemic rickets is of utmost importance as it may prevent subsequent sequelae. This report aims at warning pediatricians to consider the presence of the disease. Case description: Description of the metabolic profile, creatinine clearance, nutritional status, weight and body structure of a patient who presented the clinical-laboratorial characteristics of hypophosphatemic rickets and was followed in an outpatient clinic for tubulopathies over the period of 12 months. The patient had been bedridden for some time, was dependent on mechanical ventilation and presented an altered metabolic bone condition. Treatment was phosphate (initial: 65 mg/kg/day and final: 24,2 mg/kg/day), calcium (initial: 127 mg/kg/day, final: 48,4 mg/kg/day) and calcitriol (initial: 0.06 mcg/kg/day, final: 0.03 mcg/kg/day). The patient improved, evolving into spontaneous breathing and walking unaided. Laboratory results: calcium (mg/dL) initial 7.1, final 10.1; phosphate (mg/dL) initial 1.7 final 3.2; magnesium (mg/dL) initial 1.5 final 2.1, parathyroid hormone (pg/l) initial 85.8, final 52.7, alkaline phosphatase (UI/l) initial 12660, final 938; there was also improvement in weight/structural development (Z score: H/A initial: -6.05, final -3.64; W/A: initial -2.92, final -1.57) with presence of transitory gallstones. Creatinine clearance (mL/min/1.73m2bsa) was constant. The medication improved his laboratory results and nutritional status, but the patient did not return for two years for follow-up and, during this period, his condition has noticeably deteriorated. Comments: Early diagnosis and follow-up are essential in dealing with this pathology.
Growing scale-free networks with tunable clustering.

We extend the standard scale-free network model to include a "triad formation step. " We analyze the geometric properties of networks generated by this algorithm both analytically and by numerical calculations, and find that our model possesses the same characteristics as the standard scale-free networks such as the power-law degree distribution and the small average geodesic length, but with the high clustering at the same time. In our model, the clustering coefficient is also shown to be tunable simply by changing a control parameter---the average number of triad formation trials per time step.
Management of Rheumatoid Arthritis: Consensus Recommendations From the Turkish League Against Rheumatism

1Department of Physical Medicine and Rehabilitation, Medical Faculty of Ankara University, Division of Rheumatology, Ankara, Turkey; 2Department of Physical Medicine and Rehabilitation, Ankara Training and Research Hospital, Ankara, Turkey; 3Department of Therapy and Rehabilitation, Ankara University, Haymana Vocational School, Ankara, Turkey; 4Department of Physical Medicine and Rehabilitation, Medical Faculty of Yeditepe University, Istanbul, Turkey; 5Department of Physical Medicine and Rehabilitation, Medical Faculty of Ankara University, Ankara, Turkey; 6Department of Physical Medicine and Rehabilitation, Ankara Numune Education and Research Hospital, Ankara, Turkey; 7Department of Physical Medicine and Rehabilitation, Medical Faculty of Inonu University, Malatya, Turkey; 8Department of Physical Medicine and Rehabilitation, Medical Faculty of Trakya University, Edirne, Turkey; 9Department of Physical Medicine and Rehabilitation, Medical Faculty of Akdeniz University, Division of Rheumatology, Antalya, Turkey; 10Department of Physical Medicine and Rehabilitation, Medical Faculty of Celal Bayar University, Division of Rheumatology, Manisa, Turkey; 11Department of Physical Medicine and Rehabilitation, Medical Faculty of Gazi University, Division of Rheumatology, Ankara, Turkey; 12Department of Physical Medicine and Rehabilitation, Izmir Bozyaka Training and Research Hospital, Izmir, Turkey; 13Department of Physical Medicine and Rehabilitation, Van Training and Research Hospital, Division of Rheumatology, Van, Turkey; 14Department of Physical Medicine and Rehabilitation, Medical Faculty of Cumhuriyet University, Division of Rheumatology, Sivas, Turkey; 15Department of Physical Medicine and Rehabilitation, Izmir Ataturk Training and Research Hospital, Izmir, Turkey; 16Istanbul Physical Medicine and Rehabilitation Training and Research Hospital, Istanbul, Turkey; 17Department of Physical Medicine and Rehabilitation, Medical Faculty of Bezmialem Vakif University, Istanbul, Turkey; 18Department of Physical Medicine and Rehabilitation, Medical Faculty of Suleyman Demirel University, Isparta, Turkey; 19Department of Physical Medicine and Rehabilitation, Medical Faculty of Erciyes University, Division of Rheumatology, Kayseri, Turkey;
Successful Robotic Gastrectomy Does Not Require Extensive Laparoscopic Experience

Purpose We evaluated the learning curve and short-term surgical outcomes of robot-assisted distal gastrectomy (RADG) performed by a single surgeon experienced in open, but not laparoscopic, gastrectomy. We aimed to verify the feasibility of performing RADG without extensive laparoscopic experience. Materials and Methods Between July 2012 and December 2016, 60 RADG procedures were performed by a single surgeon using the da Vinci® Surgical System (Intuitive Surgical). Patient characteristics, the length of the learning curve, surgical parameters, and short-term postoperative outcomes were analyzed and compared before and after the learning curve had been overcome. Results The duration of surgery rapidly decreased from the first to the fourth case; after 25 procedures, the duration of surgery was stabilized, suggesting that the learning curve had been overcome. Cases were divided into 2 groups: 25 cases before the learning curve had been overcome (early cases) and 35 later cases. The mean duration of surgery was 420.8 minutes for the initial cases and 281.7 minutes for the later cases (P<0.001). The console time was significantly shorter during the later cases (168.6 minutes) than during the early cases (247.1 minutes) (P<0.001). Although the volume of blood loss during surgery declined over time, there was no significant difference between the early and later cases. No other postoperative outcomes differed between the 2 groups. Pathology reports revealed the presence of mucosal invasion in 58 patients and submucosal invasion in 2 patients. Conclusions RADG can be performed safely with acceptable surgical outcomes by experts in open gastrectomy.
Breast milk polyunsaturated fatty acids: associations with adolescent allergic disease and lung function

It has been hypothesized that n−3 PUFA in breast milk may assist immune and lung development. There are very limited data on possible long‐term effects on allergic disease and lung function. The aim was to investigate associations of n−3 and n−6 PUFA levels in colostrum and breast milk with allergic disease and lung function at ages 12 and 18 years.
Gauging the quality and trustworthiness in the citation practices of Malaysian academic researchers

The origin of this research is illuminated by CIBER's exploratory research on Trust in Scholarly Communications conducted in 2012-2013. This study's interest lies with Malaysian academic researchers both as producers and consumers and how they deal with the quality and trust consequences of the digital transition, especially, but not exclusively, the impact of social media and open access publishing on their scholarly communications. This paper reports on a survey on citation behaviour, part of a wider study of gauging quality and trustworthiness in scholarly communication in the emerging digital environment. It focuses on investigating what Malaysian researchers trust or find reliable to cite in their publications. In order to make the study results comparable, we adapted the same questionnaire that CIBER has developed and used in previous surveys. We used surveymonkey.com. a web-based questionnaire which has been widely used for surveys. The questionnaire went online on the 1 October 2014 and closed on the 30 December 2014. More than 400 respondents completed the questionnaire. The answers were analysed quantitatively and then grouped under descriptive headings of the types of reasons for citation provided. Similar to CIBER's study, the motivations for citing were found to be complex and multi-faceted but, in nearly all cases, researchers do regard the authority and trustworthiness of the cited source as an important factor in choosing to cite it. Citing behaviour includes an acknowledgement of useful intellectual content, and this process cannot be separated from the researcher's position in networks of trusted social and research influence. The digital transition has provided tools to help maintain and develop these social networks and it has also made it easier for researchers to investigate the credentials of the sources of documents. Peer-reviewed journals still hold influential. Measures of establishing trust and authority do not seem to have changed profoundly in Malaysia. The digital environment may bring ease and convenience to scholarly communication, but it gives more pressure for scholarly communication on high quality platforms. Looking at the researchers' trust-related views, it is emphasised that academic librarians apply their understanding of scholarly communication towards delivering the right services to meet the needs of the academic community.
Using Eye Gaze Data and Visual Activities to Infer Human Cognitive Styles: Method and Feasibility Studies

Recent research provides evidence that individual differences in human cognitive styles affect user performance and experience in diverse application domains. However, state-of-the-art elicitation methods of cognitive styles require researchers to apply explicit, in-lab, and time-consuming "paper-and-pencil" techniques, rendering real-time integration of cognitive styles? elicitation impractical in interactive system design. Aiming to elaborate an implicit elicitation method of cognitive styles, this paper reports two feasibility studies based on an eye-tracking multifactorial model. In both studies, participants performed visual activities of varying characteristics, and the eye-tracking analysis revealed quantitative differences on visual behavior among individuals with different cognitive styles. Based on these differences, a series of classification experiments were conducted, and the results revealed that gaze-based implicit elicitation of cognitive styles in real-time is feasible, which could be used by interactive systems to adapt to the users' cognitive needs and preferences, to better assist them, and improve their performance and experience.
Hierarchical mutational events compensate for glutamate auxotrophy of a Bacillus subtilis gltC mutant

Glutamate is the major donor of nitrogen for anabolic reactions. The Gram-positive soil bacterium Bacillus subtilis either utilizes exogenously provided glutamate or synthesizes it using the gltAB-encoded glutamate synthase (GOGAT). In the absence of glutamate, the transcription factor GltC activates expression of the GOGAT genes for glutamate production. Consequently, a gltC mutant strain is auxotrophic for glutamate. Using a genetic selection and screening system, we could isolate and differentiate between gltC suppressor mutants in one step. All mutants had acquired the ability to synthesize glutamate, independent of GltC. We identified (i) gain-of-function mutations in the gltR gene, encoding the transcription factor GltR, (ii) mutations in the promoter of the gltAB operon and (iii) massive amplification of the genomic locus containing the gltAB operon. The mutants belonging to the first two classes constitutively expressed the gltAB genes and produced sufficient glutamate for growth. By contrast, mutants that belong to the third class appeared most frequently and solved glutamate limitation by increasing the copy number of the poorly expressed gltAB genes. Thus, glutamate auxotrophy of a B. subtilis gltC mutant can be relieved in multiple ways. Moreover, recombination-dependent amplification of the gltAB genes is the predominant mutational event indicating a hierarchy of mutations.
Insights at morphological features of Contracaecum rudolphii Hartwich, 1964 (Nematoda: Anisakidae) as revealed by scanning electron microscope (SEM)

The present study provides morphological description of adults (male and female) of Contracaecum rudolphii Hartwich, 1964 collected from the proventriculus and ventriculus of the cormorant Phalacrocorax carbo (Linnaeus, 1758) in Iraq using scanning electron microscopy (SEM) showing the structures of cephalic extremity of the nematode, labium, interlabium, papillae in the dorsal labium, the morphology of caudal papillae in male, phasmids, the shape of the tip of spicule which considers as a characteristic feature of this species. A comparison with previous studies is provided.
Impact of anthropogenic emission on air quality over a megacity – revealed from an intensive atmospheric campaign during the Chinese Spring Festival

Abstract. The Chinese Spring Festival is one of the most important traditional festivals in China. The peak transport in the Spring Festival season (spring travel rush) provides a unique opportunity for investigating the impact of human activity on air quality in the Chinese megacities. Emission sources are varied and fluctuate greatly before, during and after the Festival. Increased vehicular emissions during the "spring travel rush" before the 2009 Festival resulted in high level pollutants of NOx (270 μg m−3), CO (2572 μg m−3), black carbon (BC) (8.5 μg m−3) and extremely low single scattering albedo of 0.76 in Shanghai, indicating strong, fresh combustion. Organics contributed most to PM2.5, followed by NO3−, NH4+, and SO42−. During the Chinese Lunar New Year's Eve and Day, widespread usage of fireworks caused heavy pollution of extremely high aerosol concentration, scattering coefficient, SO2, and NOx. Due to the "spring travel rush" after the festival, anthropogenic emissions gradually climbed and mirrored corresponding increases in the aerosol components and gaseous pollutants. Secondary inorganic aerosol (SO42−, NO3−, and NH4+) accounted for a dominant fraction of 74% in PM2.5 due to an increase in human activity. There was a greater demand for energy as vast numbers of people using public transportation or driving their own vehicles returned home after the Festival. Factories and constructions sites were operating again. The potential source contribution function (PSCF) analysis illustrated the possible source areas for air pollutants of Shanghai. The effects of regional and long-range transport were both revealed. Five major sources, i.e. natural sources, vehicular emissions, burning of fireworks, industrial and metallurgical emissions, and coal burning were identified using the principle component analysis. The average visibility during the whole study period was less than 6 km. It had been estimated that 50% of the total light extinction was due to the high water vapor in the atmosphere. This study demonstrates that organic aerosol was the largest contributor to aerosol extinction at 47%, followed by sulfate ammonium, nitrate ammonium, and EC at 22%, 14%, and 12%, respectively. Our results indicated the dominant role of traffic-related aerosol species (i.e. organic aerosol, nitrate and EC) on the formation of air pollution, and suggested the importance of controlling vehicle numbers and emissions in mega-cities of China as its population and economy continue to grow.
Automatic generation of coarse bounding cages from dense meshes

The coarse bounding cage of a dense mesh plays important roles in computer graphics, computer vision, and geometric design. Specifically, in volume-based deformation, a coarse bounding cage is required to manipulate the dense mesh model it enclosed; in subdivision surface fitting, the fitting starts from a coarse cage bounding the fitted dense mesh or point set; and so on. However, the generation of a coarse bounding cage is mainly by interactive ways, which are very tedious and time-consuming. In this paper, we develop a fully automatic method to generate a coarse cage bounding a dense mesh model. The automatically generated coarse bounding cage can keep the topological structure and major geometric features of the original mesh model, which is validated by theoretical analysis and experimental data presented in this paper. Further more, we employ the automatically generated coarse bounding cage in some applications, such as deformation, and subdivision fitting, producing good results.
Perlecan/HSPG2 and matrilysin/MMP-7 as indices of tissue invasion: tissue localization and circulating perlecan fragments in a cohort of 288 radical prostatectomy patients

Prostate cancer (PCa) cells use matrix metalloproteinases (MMPs) to degrade tissue during invasion. Perlecan/HSPG2 is degraded at basement membranes, in reactive stroma and in bone marrow during metastasis. We previously showed MMP-7 efficiently degrades perlecan. We now analyzed PCa tissue and serum from 288 prostatectomy patients of various Gleason grades to decipher the relationship between perlecan and MMP-7 in invasive PCa. In 157 prostatectomy specimens examined by tissue microarray, perlecan levels were 18% higher than their normal counterparts. In Gleason grade 4 tissues, MMP-7 and perlecan immunostaining levels were highly correlated with each other (average correlation coefficient of 0.52) in PCa tissue, regardless of grade. Serial sections showed intense, but non-overlapping, immunostaining for MMP-7 and perlecan at adjacent borders, reflecting the protease-substrate relationship. Using a capture assay, analysis of 288 PCa sera collected at prostatectomy showed elevated levels of perlecan fragments, with most derived from domain IV. Perlecan fragments in PCa sera were associated with overall MMP-7 staining levels in PCa tissues. Domain IV perlecan fragments were present in stage IV, but absent in normal, sera, suggesting perlecan degradation during metastasis. Together, perlecan fragments in sera and MMP-7 in tissues of PCa patients are measures of invasive PCa.
IDH1/2 Mutations Sensitize Acute Myeloid Leukemia to PARP Inhibition and This Is Reversed by IDH1/2-Mutant Inhibitors

Purpose: Somatic mutations in IDH1/2 occur in approximately 20% of patients with myeloid neoplasms, including acute myeloid leukemia (AML). IDH1/2MUT enzymes produce D-2-hydroxyglutarate (D2HG), which associates with increased DNA damage and improved responses to chemo/radiotherapy and PARP inhibitors in solid tumor cells. Whether this also holds true for IDH1/2MUT AML is not known. Experimental Design: Well-characterized primary IDH1MUT, IDH2MUT, and IDH1/2WT AML cells were analyzed for DNA damage and responses to daunorubicin, ionizing radiation, and PARP inhibitors. Results: IDH1/2MUT caused increased DNA damage and sensitization to daunorubicin, irradiation, and the PARP inhibitors olaparib and talazoparib in AML cells. IDH1/2MUT inhibitors protected against these treatments. Combined treatment with a PARP inhibitor and daunorubicin had an additive effect on the killing of IDH1/2MUT AML cells. We provide evidence that the therapy sensitivity of IDH1/2MUT cells was caused by D2HG-mediated downregulation of expression of the DNA damage response gene ATM and not by altered redox responses due to metabolic alterations in IDH1/2MUT cells. Conclusions: IDH1/2MUT AML cells are sensitive to PARP inhibitors as monotherapy but especially when combined with a DNA-damaging agent, such as daunorubicin, whereas concomitant administration of IDH1/2MUT inhibitors during cytotoxic therapy decrease the efficacy of both agents in IDH1/2MUT AML. These results advocate in favor of clinical trials of PARP inhibitors either or not in combination with daunorubicin in IDH1/2MUT AML. Clin Cancer Res; 24(7); 1705–15. ©2018 AACR.