nils-herrmann/clean_scirepeval huggingface dataset:
Chemical Probes Reveal Sirt2's New Function as a Robust "Eraser" of Lysine Lipoylation.
Venue: Journal of the American Chemical Society
Year: 2019

Lysine lipoylation, a highly conserved lysine PTM, plays a critical role in regulating cell metabolism. The catalytic activity of a number of vital metabolic proteins, such as pyruvate dehydrogenase (PDH) depends on lysine lipoylation. Despite its important roles, the detailed biological regulatory mechanism of lysine lipoylation remains largely unexplored. Herein we designed a powerful affinity based probe KPlip to interrogate the interactions of lipoylated peptide/proteins under native cellular environment. Large scale chemical proteomics analysis revealed a number of binding proteins of KPlip, including Sirt2, an NAD+ dependent protein deacylase. To explore the potential activity of Sirt2 toward lysine lipoylation, we designed a single step fluorogenic probe KTlip, which reports delipoylation activity in a continuous manner. The results showed that Sirt2 led to significant delipoylation of KTlip, displaying up to 60 fold fluorescence increase in the assay. Further kinetic experiments with different peptide substrates revealed that Sirt2 can catalyze the delipoylation of peptide (DLAT PDH, K259) with a remarkable catalytic efficiency (kcat/Km) of 3.26 x 103 s 1M 1. The activity is about 400 fold higher than that of Sirt4, the only mammalian enzyme with known delipoylation activity. Furthermore, overexpression and silencing experiments demonstrated that Sirt2 regulates the lipoylation level and the activity of endogenous PDH, thus unequivocally confirming that PDH is a genuine physiological substrate of Sirt2. Using our chemical probes, we have successfully established the relationship between Sirt2 and lysine lipoylation in living cells for the first time. We envision that such chemical probes will serve as useful tools for delineating the roles of lysine lipoylation in biology and diseases.
Increased expression of programmed cell death protein 1 on NK cells inhibits NK cell mediated anti tumor function and indicates poor prognosis in digestive cancers
Venue: Oncogene
Year: 2017

Abnormal expression of activating/inhibitory receptors leads to natural killer (NK) cells dysfunction in tumor. Here we show that programmed cell death protein 1 (PD 1) a well known immune checkpoint of T cells, is highly expressed on peripheral and tumor infiltrating NK cells from patients with digestive cancers including esophageal, liver, colorectal, gastric and biliary cancer. The increased PD 1 expression on NK cells indicates poorer survival in esophageal and liver cancers. Blocking PD 1/PD L1 signaling markedly enhances cytokines production and degranulation and suppresses apoptosis of NK cells in vitro. PD 1/PD L1 exerts inhibitory effect through repressing the activation of PI3K/AKT signaling in NK cells. More importantly, a PD 1 blocking antibody was found to significantly suppress the growth of xenografts in nude mice, and this inhibition of tumor growth was completely abrogated by NK depletion. These findings strongly suggested that PD 1 is an inhibitory regulator of NK cells in digestive cancers. PD 1 blockade might be an efficient strategy in NK cell based tumor immunotherapy.
A Cluster of Novel Coronavirus Disease 2019 Infections Indicating Person to Person Transmission Among Casual Contacts From Social Gatherings: An Outbreak Case Contact Investigation
Venue: Open forum infectious diseases
Year: 2020

Severe acute respiratory syndrome coronavirus 2, the pathogen causing novel coronavirus disease of 2019 (COVID 19) efficiently spreads from person to person in close contact settings. Transmission among casual contacts in settings such as during social gatherings is not well understood.  We report several transmission events to both close and casual contacts from a cluster of 7 COVID 19 cases occurring from mid January to early February 2020. A total of 539 social and family contacts of the index patient's, including members of a 2 day wedding and a family party, were contacted and screened through epidemiologic surveys. The clinical progression of all cases is described.  We estimate the secondary attack rate among close contacts to be 29% (2 of 7) and for the casual contacts to be 0.6% (3 of 473) The incubation period of our case cluster was 4 12 days (median, 7 days)  Transmission efficiency among close contacts was higher than among casual contacts; however, transmission from second generation cases may help spread the virus during the incubation period.
Effect of water sludge ratio and reaction time on the hydrothermal carbonization of olive oil mill wastewater treatment: Hydrochar characterization
Venue: Journal of Water Process Engineering
Year: 2019

Hydrothermal carbonization (HTC) was used to treat olive oil mill wastewater (OOMW) by using water in the absence of any additional reagent. The reaction time and the water sludge (W/S) ratio were varied, over a broad set of values, to study their effect on the hydrochar products. As reaction time and water sludge ratio increased, the hydrochar yield decreased from 36% to 7% In addition, HTC upgraded both carbon and energy contents to very high values, 76% and 36 MJ/kg respectively. Hence, the hydrochars products are good candidates for energy generation. Moreover, the hydrochars products were amorphous and had a hydrophobic oleophilic structure. Their quality and energy yield increased with the decrease in water sludge ratio while reaction time slightly affected the hydrochar properties. Operating the process at the lowest water sludge ratio and short reaction time leads to hydrochars with the finest characteristics but at the expense of higher cost due to evaporation rate.
PENGARUH EDUKASI GIZI MELALUI MEDIA FACEBOOK TERHADAP PENGETAHUAN ANEMIA DAN KONSUMSI PROTEIN, ZAT BESI, DAN VITAMIN C PADA REMAJA PUTRI DESA TEBAS KUALA
Year: 2019

Menurut WHO, anemia merupakan suatu kondisi dimana konsentrasi hemoglobin atau jumlah sel darah merah di bawah normal. Sedangkan definisi anemia gizi adalah keadaan dimana kadar hemoglobin, hematokrit, dan jumlah sel darah merah yang lebih rendah dari normal. Penelitian ini bertujuan untuk mengetahui perbedaan pengetahuan anemia dan konsumsi protein, zat besi, serta vitamin C sebelum dan sesudah diberikan edukasi gizi melalui media Facebook di Desa Tebas Kuala. Jenis penelitian ini adalah Eksperimental dengan rancangan one group pretest post test design. Analisis yang digunakan adalah uji normalitas Paired T Test. Populasi penelitian ini adalah remaja putri yang tinggal di wilayah Desa Tebas Kuala dengan sampel kelompok intervensi sebanyak 35 remaja putri. Hasil penelitian menunjukkan pengetahuan anemia, konsumsi protein, konsumsi zat besi, dan konsumsi vitamin C pada sampel mengalami peningkatan. Secara statistik, ada perbedaan bermakna antara pengetahuan anemia, konsumsi protein, konsumsi zat besi, dan konsumsi vitamin C pada remaja putri sebelum dan sesudah intervensi (p=0,000) Simpulan penelitian adalah adanya pengaruh edukasi gizi melalui media Facebook terhadap peningkatan pengetahuan anemia, dan konsumsi protein, konsumsi zat besi, serta konsumsi vitamin C pada remaja putri.
Active matter: from collective self propelled rods to cell like particles
Year: 2018

Active matter comprises systems with sustained energy uptake and dissipation of its constituents. This applies to systems across many scales. We study ensembles of self propelled rods (SPRs) in periodic boundaries and in confinement to mimic the collective behavior and dynamics of bacteria, and active filaments. Our models describe active systems that allow the propulsion to adapt to its environment. While SPRs with density dependent slowing down partially capture the behavior observed for bacteria, SPRs in ring like confinements can be considered as a minimal, soft matter model for cell motility. Phoretic microswimmers and genetically modified E. coli show density dependent reduced propulsion.This motivates the investigation of the collective behavior and dynamics of SPRs with density dependent propulsion force. The density dependent slowing down enhances polar ordering and cluster formation, and induces rod perpendicularity at cluster borders. As a model of cellular motility due to cytoskeletal activity, SPRs inside mobile, rigid circular confinement are considered, which build complex self propelled rings. The rod self organization gives rise to complex motility patterns, such as run and tumble and run and circle motion. Motility patterns observed for self propelled rigid rings are also observed for motile cells. Taking a further step towards a more realistic modeling of cell motility, we study SPRs inside mobile, deformable rings. In addition to ring motility, also ring deformability plays a crucial role in SPR alignment and cluster formation. Here, pulling forces at the back of the rings are crucial to recovering cell like shapes and motion. While our models do not take into account biochemical aspects of biological systems, they allow the identification of crucial mechanical aspects, and help to test different underlying mechanisms to interpret microscopic observations.
Parasocial Interaction and Narrative Involvement as Predictors of Attitude Change
Year: 2018

Parasocial interaction and the concept of entertainment education create a framework to explore how people react to persuasive messages from political commentators. The role parasocial interaction and narrative involvement play in attitude change are assessed in this essay. After considering the impact of parasocial interactions, assessments are made concerning viewers' likelihood of elaboration, attitude change, and likelihood of behavior change. Findings suggest higher PSI generates stronger support for the advocated position, and increased likelihood for attitude and likelihood of behavior change.
European Union Common Commercial Policy
Year: 2020

An effective international trade and investment policy is important for the European Union and to the EU is important for the maintenance of an open, rules based trading system. The challenges facing the trading system in terms of a structural shift in influence away from the former Quad (the USA, EU, Japan and Canada) as well as mercantilist and populist tendencies in some major trading partners call for a strategic response from the EU. At the same time domestic demands for greater transparency and democratic control of the Common Commercial Policy (CCP) are a potential brake on the ability of the EU to act. At issue therefore is how the EU can reconcile these international and domestic dimensions of policy so that the credibility of the EU as a leading actor in the international trade and investment is not undermined or questioned. To date the modifications of the CCP in the Lisbon Treaty have managed to cope reasonably well, but EU institutions and in particular the Member State governments need to engage more in a public debate on the aims and limitations of the CCP.
Hydrogen sulfide improves diabetic wound healing in ob/ob mice via attenuating inflammation.
Venue: Journal of diabetes and its complications
Year: 2017

The proposed mechanisms of impaired wound healing in diabetes involve sustained inflammation, excess oxidative stress and compromised agiogenesis. Hydrogen sulfide (H2S) has been reported to have multiple biological activities. We aim to investigate the role of H2S in impaired wound healing in ob/ob mice and explore the possible mechanisms involved. PROCEDURES Full thickness skin dorsal wounds were created on ob/ob mice and C57BL/6 mice. Cystathionine g lyase (CSE) expression and H2S production were determined in granulation tissues of the wounds. Effects of NaHS on wound healing were evaluated. Inflammation and angiogenesis in granulation tissues of the wounds were examined.  CSE expression, and H2S content were significantly reduced in granulation tissues of wounds in ob/ob mice compared with control mice. NaHS treatment significantly improved wound healing in ob/ob mice, which was associated with reduced neutrophil and macrophage infiltration, decreased production of tumor necrosis factor (TNF) a, interleukin (IL) 6. NaHS treatment decreased metalloproteinase (MMP) 9, whereas increased collagen deposition and vascular like structures in granulation tissues of wounds in ob/ob mice.  CSE down regulation may play a role in the pathogenesis of diabetic impaired wound healing. Exogenous H2S could be a potential agent to improve diabetic impaired wound healing by attenuating inflammation and increasing angiogenesis.
Power system transient stability analysis using matlab software
Year: 2013

The electric market liberalization increases its importance, as economical pressure and intensified transactions tend to operate electric power systems much closer to their security limits than ever before. The trend to merge existing systems into much larger entities and to monitor them in shorter and shorter time horizons creates more difficulties. This holds true for analysis aspects and even more for control, in as much as, today; control actions must cope with considerably more stringent market requirements than in the past. The difficulties increase further when it comes to transient stability phenomena. This thesis has discussed some theory related to transient stability such as the swing equation, transfer reactance, power angle curve and equal area criterion. In this thesis two possible methods of transient stability have been discussed and they are step by step solution for swing curve and equal area criterion. Some MATLAB programs have been developed to study the transient stability cases by using these two methods. For first method, the transient studies are conducted in two cases. For case 1, the fault cleared at time t 0.2 second and the second case 2 where the fault cleared at time t =0.4 second. For second method of equal area criterion has three case studies. All the input are same accept for sudden increase in power generator which for case 3 is 0.9 p.u, case 4 is 1.099 p.u and case 5 is 1.1 p.u. Lastly for case 6 and 7 the application of equal area criterion to three phase fault were investigate the fault at the sending end of the line and fault at some distance away from the sending end. These programs are helpful in determining critical power angle, critical clearing times for circuit breaker, voltage level of systems and transfer capability between systems. Thus, a better relay setting can be proposed.
Origin and fate of organic compounds in water: characterization by compound specific stable isotope analysis.
Venue: Annual review of analytical chemistry
Year: 2012

Within the past 15 years, compound specific stable isotope analysis has continued to increase in popularity in the area of contaminant hydrology of organic molecules. In particular, in cases where concentration data alone are insufficient to elucidate environmental processes unequivocally, the isotope signature can provide additional unique information. Specifically, it can help answer questions about contaminant source apportionment, quantification of biotic and abiotic processes, and identification of transformation reactions on a mechanistic level. We review advances in laboratory and field investigations and exemplary applications in contaminant hydrology via stable isotope analysis. We also highlight future directions in the field.
Western music and municipality in 1930s and 1940s Shanghai
Year: 2017

Acknowledgements Note on Chinese Characters List of Figures Prologue 12 '1930s and 1940s Shanghai' A Socio Musicological Inquiry Chapter 1 50 International Settlement (Treaty Port I) 'Trying to listen to the music' Shanghailanders, Parks, The Shanghai Municipal Brass Band Chapter 2 89 French Concession (Treaty Port II) 'Aucun instrument de cuivre' Colonial Rule, Licensed Venues, Musical Soundscape Chapter 3 124 Japanese Occupied Shanghai, 'Die gute Unterhaltungsmusik' Landscape, Refugee Cafes, Sounds of 'Little Vienna' Chapter 4 174 Nationalist Shanghai, 'Nightclub Cafe' Taxable Eateries and Claims of a Distinct Musical Sound Epilogue 210 Beyond '1930s and 1940s Shanghai' Reproduction Maps, Repositories, Archival Musicology
Gender action plans in the aquaculture value chain: what's missing?
Year: 2019

Gender equality has been a political issue in view of human rights and welfare since several decades. Therefore, many countries have developed Gender Action Plans (GAPs) that support equal access of both sexes to education, employment and finance. Two workshops on GAPs in aquaculture and a literature review brought about the question: what's missing in Asian sectoral GAPs. Not all reviewed Asian countries have GAPs for fishery/ aquaculture, but all encountered constraints to achieve their goals regarding equal access for women. Women's contribution in aquaculture tends to go beyond the traditional gender divide. For example, women may lead in the area of production because they can combine aquaculture with their homebound tasks and own vertically integrated companies. However, skewed perceptions on the role, status and perception of women and men, more so in strong than weak patriarchies (the former accept the subservient role, while the latter exercise the dominant role) limit women's access to training opportunities on new aquaculture technologies. Women are also left out in policy and decision making processes; and in the value chain, women receive lower wages than men. Their role is underestimated by lack of disaggregated data, as reflected in post disaster interventions and industrial development programs. To be effective sectoral GAPs, based on disaggregated data, should have budgets, plans and target indicators for which leaders could be held accountable. These GAPs, however, can't address the required radical change in attitude toward women; unless deliberately planned educational media campaigns are embedded into the national GAPs.
Comparison of low dose CT with CT/CT Fluoroscopy guidance in percutaneous sacral and supra acetabular cementoplasty.
Venue: Diagnostic and interventional radiology
Year: 2019

Percutaneous cementoplasty is a minimally invasive treatment modality for painful osteoporotic and pathologic sacral and supra acetabular iliac fractures. This study compares the use of low dose CT guidance with CT/CT fluoroscopy in sacral and supra acetabular cementoplasty.  A retrospective review of patients who had undergone sacral or supra acetabular cementoplasty was performed with patients grouped by use of CT/CT Fluoroscopy or low dose CT guidance during the procedure. Parameters evaluated included type of fracture, laterality of lesions, pain scores, pain medication use, imaging parameters, procedure time, dose length product, effective dose, cement volume, and complications.  There were 17 patients identified who underwent cementoplasty utilizing dual CT/CT Fluoroscopy, while 13 patients had their procedures performed with low dose CT. There was a statistically significant decrease in radiation dose in the low dose CT group (1481 mGy cm) compared to the CT/CT Fluoroscopy group (2809mGy cm) (P 0.013) There was a significant decrease in procedure time with low dose CT for bilateral lesions (P 0.016) There was no significant difference between groups in complication rate (P 0.999) Non clinically significant cement extravasation occurred in two patients (10% in the CT/CT Fluoroscopy group and in one patient (8% in the low dose CT group (P 0.999) There was a significant decrease in pain scores compared to baseline on the Visual Analogue Scale in both groups at 1 week (low dose CT P 0.002, CT/CTF P 0.008) and 1 month post procedure (low dose CT P 0.014, CT/CTF P 0.004) but no difference between groups at 1 day (P 0.196) 1 week (P 0.368) or 1 month (P 0.514) CONCLUSION Sacral and supra acetabular cementoplasties can be performed safely and precisely using low dose multiple acquisition CT guidance while providing significant radiation dose reduction with no difference in extravasation rates, post procedural pain reduction and complications compared to CT/CT Fluoroscopy.
Identifying Predictors of Levator Veli Palatini Muscle Contraction During Speech Using Dynamic Magnetic Resonance Imaging.
Venue: Journal of speech, language, and hearing research JSLHR
Year: 2020

The purpose of this study was to identify predictors of levator veli palatini (LVP) muscle shortening and maximum contraction velocity in adults with normal anatomy.  Twenty two Caucasian English speaking adults with normal speech and resonance were recruited. Participants included 11 men and 11 women (M 22.8 years, SD 4.1) with normal anatomy. Static magnetic resonance images were obtained using a three dimensional static imaging protocol. Midsagittal and oblique coronal planes were established for visualization of the velum and LVP muscle at rest. Dynamic magnetic resonance images were obtained in the oblique coronal plane during production of "ansa." Amira 6.0.1 Visualization and Volume Modeling Software and MATLAB were used to analyze images and calculate LVP shortening and maximum contraction velocity.  Significant predictors (p .05) of maximum LVP shortening during velopharyngeal closure included mean extravelar length, LVP origin to origin distance, velar thickness, pharyngeal depth, and velopharyngeal ratio. Significant predictors (p .05) of maximum contraction velocity during velopharyngeal closure included mean extravelar length, intravelar length, LVP origin to origin distance, and velar thickness.  This study identified six velopharyngeal variables that predict LVP muscle function during real time speech. These predictors should be considered among children and individuals with repaired cleft palate in future studies.
Observations on the Therapeutic Effect of Acupuncture on Post stroke Depression
Year: 2010

To investigate the clinical therapeutic effect of acupuncture on post stroke depression. Sixty patients were randomly allocated to an acupuncture plus medicine(Prozac) group and a medication(oral administration of Prozac only) group.The HAMD scale score was counted in the two groups of patients before and after one course of treatment. Both groups obtain a certain therapeutic effect.The total efficacy rate was 93.3% in the acupuncture plus medicine group and 83.3% in the medication group;there was a statistically significant difference(P0.05).Conclusion Acupuncture has a marked therapeutic effect on post stroke depression.
Driving Force of Covid 19 Among People Living With HIV/AIDS in Wuhan, China
Venue: Research square
Year: 2020

Even people living with HIV/AIDS (PLWHA) were considered to be at increased risk of SARS CoV 2 infection, the driving force among this group of individuals is still not clear.  We investigated 1,701 PLWHA through a telephone interview and found 11 COVID 19 patients in four districts of Wuhan, China. The demographic features and major clinical characteristics of these patients were retrieved from the information management systems for COVID 19 patients of four districts' CDC. Statistical analysis was performed to find out the driving force of COVID 19 among PLWHA.  The incidence proportion of COVID 19 in PLWHA is 0.6% (95% CI: 0.2% 1.0% which is comparable to the overall population incidence rate in Wuhan city (0.6% Nine out of the 11 COVID 19/AIDS patients had relatively high CD4+ T lymphocyte count >200/ml) and undetectable HIV viral load (20 copies/ml) and ten of them were on antiretroviral therapy. PLWHA who were old, had low CD4+ T lymphocyte count, infected HIV through homosexual activity, and had been diagnosed for HIV for a long time, were more likely to develop COVID 19.  PLWHA has comparable COVID 19 morbidity rates as the general population, and older age, low CD4 count, long length since HIV diagnosis, and treatment naive were potential driving forces of COVID 19 occurrence among PLWHA. Strategies in preventing SARS CoV 2 infection among PLWHA with worse immune responses are needed.  As COVID 19 continues to spread around the world, people living with HIV/AIDS (PLWHA) are also at risk of infection with SARS CoV 2. We investigated the factors associated with SARS CoV 2 infection among PLWHA in Wuhan, China.