nils-herrmann/clean_scirepeval huggingface dataset:
Sustainable agro food supply chain design using two stage hybrid multi objective decision making approach
Venue: Comput. Oper. Res.
Year: 2018

Sustainability of agro food supply chains has recently become the subject of greater interest from consumers, firms, governmental organizations and academia as the environment continues to deteriorate. One of the most critical factors influencing the sustainability of an agro food supply chain is its network design. A particularly challenging aspect in this context is the broad range of influencing indicators associated with the Triple Bottom Line (TBL) of sustainability that need to be considered. However, many of these indicators could not be fully integrated or measured by single step optimization problems. This paper presents a critical literature review of operational research methods for the design of sustainable supply chains. A novel two stage hybrid solution methodology is proposed. In the first stage, a partner selection is performed using a hybrid multi criteria decision making based on Analytic Hierarchy Process (AHP) method and the Ordered Weighted Averaging (OWA) aggregation method. The result obtained in the first stage is used in the second stage to develop a multi objective mathematical model to optimize the design of the supply chain network. This approach allows the simultaneous consideration of all three dimensions of sustainability including carbon footprint, water footprint, number of jobs created and the total cost of the supply chain design. The proposed approach generates a Pareto frontier to aid users in making decisions. Numerical experiments are completed utilizing data from an agro food company to demonstrate the efficiency and effectiveness of the proposed solution methodology. The analyzes of the numerical results provide important organizational, practical and policy insights on (1) the impact of financial and environmental sustainability on supply chain network design (2) the tradeoff analysis between environmental emission, water footprint, societal implications and associated cost for making informed decision on supply chain investment.
Insect Gut Symbiont Susceptibility to Host Antimicrobial Peptides Caused by Alteration of the Bacterial Cell Envelope*
Venue: The Journal of Biological Chemistry
Year: 2015

The elucidation of molecular changes of symbionts is important for understanding symbiotic adaptation.  Insect gut symbionts are highly susceptible to host immunity because of dramatic cell envelope changes.  Cell envelope changes in gut symbionts are required for successful symbiosis with hosts.  Biochemical analyses of intact gut symbionts revealed a novel mechanism of gut symbiosis. The molecular characterization of symbionts is pivotal for understanding the cross talk between symbionts and hosts. In addition to valuable knowledge obtained from symbiont genomic studies, the biochemical characterization of symbionts is important to fully understand symbiotic interactions. The bean bug (Riptortus pedestris) has been recognized as a useful experimental insect gut symbiosis model system because of its cultivatable Burkholderia symbionts. This system is greatly advantageous because it allows the acquisition of a large quantity of homogeneous symbionts from the host midgut. Using these naive gut symbionts, it is possible to directly compare in vivo symbiotic cells with in vitro cultured cells using biochemical approaches. With the goal of understanding molecular changes that occur in Burkholderia cells as they adapt to the Riptortus gut environment, we first elucidated that symbiotic Burkholderia cells are highly susceptible to purified Riptortus antimicrobial peptides. In search of the mechanisms of the increased immunosusceptibility of symbionts, we found striking differences in cell envelope structures between cultured and symbiotic Burkholderia cells. The bacterial lipopolysaccharide O antigen was absent from symbiotic cells examined by gel electrophoretic and mass spectrometric analyses, and their membranes were more sensitive to detergent lysis. These changes in the cell envelope were responsible for the increased susceptibility of the Burkholderia symbionts to host innate immunity. Our results suggest that the symbiotic interactions between the Riptortus host and Burkholderia gut symbionts induce bacterial cell envelope changes to achieve successful gut symbiosis.
Targeting BER enzymes in cancer therapy.
Venue: DNA repair
Year: 2018

Base excision repair (BER) repairs mutagenic or genotoxic DNA base lesions, thought to be important for both the etiology and treatment of cancer. Cancer phenotypic stress induces oxidative lesions, and deamination products are responsible for one of the most prevalent mutational signatures in cancer. Chemotherapeutic agents induce genotoxic DNA base damage that are substrates for BER, while synthetic lethal approaches targeting BER related factors are making their way into the clinic. Thus, there are three strategies by which BER is envisioned to be relevant in cancer chemotherapy: (i) to maintain cellular growth in the presence of endogenous DNA damage in stressed cancer cells, (ii) to maintain viability after exogenous DNA damage is introduced by therapeutic intervention, or (iii) to confer synthetic lethality in cancer cells that have lost one or more additional DNA repair pathways. Here, we discuss the potential treatment strategies, and briefly summarize the progress that has been made in developing inhibitors to core BER proteins and related factors.
De l'impact des RPC pour reduire le taux d'episiotomie
Year: 2012

Following the publication of the French Guidelines on episiotomy in 2005 by the French National College of Gynaecologists and Obstetricians (CNGOF) our unit decided to adopt a restrictive politics to replace the former liberal one. The goal of this study was to evaluate the impact of this modification of trend in the Unit of Gynaecology and Obstetrics of the teaching hospital from Caen. This was the start point of an internal audit with the objective of an enhancement of the care during delivery.  It was a retrospective study concerning the period going from January, 2004 till December, 2009, measuring the impact of the guidelines on the episiotomy rates and perineal tears. The totality of the population of the women naturally delivered at a term superior or equal to 37 weeks of gestation and a cephalic presentation was included. To modify the practices, after diffusion of the guidelines by some obstetrical leaders, we imposed to notify the indication of the episiotomy in the computerized obstetrical files. Moreover, we published monthly screenboards with all the detailed results to all the practioners acting in the delivery room (obstetricians, midwives)  Between 2004 and 2009, we observed a dramatic decline of the episiotomy rates from 55.7 to 13.3% This trend was the same for primiparae and multiparae, as wall as for spontaneous or assisted delivery (mostly vacuum extraction in our unit) We noticed a slight increased in minor perineal tears without functional consequences. There was no statistically significant difference between severe perineal tear (1.3% vs. 1.1% By contrary, the rate of intact perineum significantly raised (17.6% vs. 21.7% p<0.001) especially in vacuum extractions.  Our results are in accordance with those of the national guidelines. However, our rate does not decrease in 2007 and 2008 (20% contrary to some results obtained in the literature. Some reports mentioned the weak impact of the publication of national guidelines to modify the usual practice. However, we believe that retro information to practitioners has a real impact on their daily current practice. Hence we insisted again on the importance of these national guidelines at the end of 2008 and we could demonstrate a real decline of the rate of episiotomy. Our efforts have to be continued, especially for instrumental delivery.
Palonosetron attenuates 1,2 dimethyl hydrazine induced preneoplastic colon damage through downregulating acetylcholinesterase expression and up regulating synaptic acetylcholine concentration
Year: 2016

The present study was undertaken to evaluate the effect of palonosetron (PAL) against 1,2 dimethylhydrazine (DMH) induced colon cancer. Wistar albino rats were randomly divided into four groups (n 8) Group 1 served as normal control (1 mM EDTA saline, 2 ml per kg per day, s.c. group 2 toxic control; group 2, 3 and 4 received DMH (20 mg per kg per week, s.c. for 6 weeks; groups 3 and 4 also received PAL (0.25 and 0.50 mg per kg per day, p.o) for 6 weeks. DMH treated rats showed altered heart rate variability (HRV) factors, increased incidence of aberrant crypt foci (ACF) distorted antioxidant markers (TBAR's, SOD, catalase, GSH) and increased levels inflammatory markers (COX) The colonic surface architecture, studied using scanning electron microscopy (SEM) revealed aberrant crypts (500x) and preneoplastic nodules (2000x) PAL treatment helped to minimize the ACF count, and restored oxidative and inflammatory markers favorably. To further validate our results, we directed our study to define the effect of PAL on acetylcholine (Ach) neurotransmission using a simple model organism, C. elegans. Increased cholinergic transmission by PAL (8 mM) was evident in the worms when studied through an aldicarb assay. However, PAL (2 mM, 4 mM and 8 mM) treatment negatively modulated nAchR, when evaluated using the levamisole assay. The increased synaptic Ach levels can be attributed to the decreased levels of acetylcholinesterase (AchE) which could be attributed to the decreased genomic levels of ace 1 and ace 2. The above findings were also supported by the fact, that we observed decreased AchE activity in PAL treated rats. In addition the downregulation in the expression of unc 38 (one of the necessary components of nAchR) sufficiently links with the decreased nAchR activity. Our findings emphasize the potential role of PAL in the suppression of colon carcinogenesis.
A Few shot Learning Approach for Historical Ciphered Manuscript Recognition
Venue: 2020 25th International Conference on Pattern Recognition (ICPR)
Year: 2021

Encoded (or ciphered) manuscripts are a special type of historical documents that contain encrypted text. The automatic recognition of this kind of documents is challenging because: 1) the cipher alphabet changes from one document to another, 2) there is a lack of annotated corpus for training and 3) touching symbols make the symbol segmentation difficult and complex. To overcome these difficulties, we propose a novel method for handwritten ciphers recognition based on few shot object detection. Our method first detects all symbols of a given alphabet in a line image, and then a decoding step maps the symbol similarity scores to the final sequence of transcribed symbols. By training on synthetic data, we show that the proposed architecture is able to recognize handwritten ciphers with unseen alphabets. In addition, if few labeled pages with the same alphabet are used for fine tuning, our method surpasses existing unsupervised and supervised HTR methods for ciphers recognition.
Magnetic domain wall conduits for single cell applications.
Venue: Lab on a chip
Year: 2011

The ability to trap, manipulate and release single cells on a surface is important both for fundamental studies of cellular processes and for the development of novel lab on chip miniaturized tools for biological and medical applications. In this paper we demonstrate how magnetic domain walls generated in micro and nano structures fabricated on a chip surface can be used to handle single yeast cells labeled with magnetic beads. In detail, first we show that the proposed approach maintains the microorganism viable, as proven by monitoring the division of labeled yeast cells trapped by domain walls over 16 hours. Moreover, we demonstrate the controlled transport and release of individual yeast cells via displacement and annihilation of individual domain walls in micro and nano sized magnetic structures. These results pave the way to the implementation of magnetic devices based on domain walls technology in lab on chip systems devoted to accurate individual cell trapping and manipulation.
A Distributed Predictive Control Approach for Cooperative Manipulation of Multiple Underwater Vehicle Manipulator Systems
Venue: 2019 International Conference on Robotics and Automation (ICRA)
Year: 2019

This paper addresses the problem of cooperative object transportation for multiple Underwater Vehicle Manipulator Systems (UVMSs) in a constrained workspace involving static obstacles. We propose a Nonlinear Model Predictive Control (NMPC) approach for a team of UVMSs in order to transport an object while avoiding significant constraints and limitations such as: kinematic and representation singularities, obstacles within the workspace, joint limits and control input saturations. More precisely, by exploiting the coupled dynamics between the robots and the object, and using certain load sharing coefficients, we design a distributed NMPC for each UVMS in order to cooperatively transport the object within the workspace's feasible region. Moreover, the control scheme adopts load sharing among the UVMSs according to their specific payload capabilities. Additionally, the feedback relies on each UVMS's locally measurements and no explicit data is exchanged online among the robots, thus reducing the required communication bandwidth. Finally, real time simulation results conducted in UwSim dynamic simulator running in ROS environment verify the efficiency of the theoretical finding.
Fabrication of a vermifiltration unit for wastewater recycling and performance of vermifiltered water (vermiaqua) on onion (Allium cepa)
Venue: International Journal of Recycling of Organic Waste in Agriculture
Year: 2019

PurposeVemifiltration units are sludge free, noise free and low or no electricity requiring systems of operation. The aim of this study was to emphasize wastewater treatment by vermifiltration technology using waste eater earthworms to highlight the benefits of clean and nutritive vermifiltered water (vermiaqua) uses in agriculture to the farmers.MethodsWastewater sample was filtered through fabricated vermifiltration unit to study physio chemical and biological properties of vermiaqua and uniform sized Allium cepa (Onion) bulbs were kept for root germination at different concentrations (10 1, 10 3, 10 5, 10 7, 10 9) of wastewater and vermiaqua at room temperature for 5 days to study impacts of vermiaqua on morphological and cytological characteristics of onion.ResultsVermiaqua was odorless, pale yellow in appearance, lower in turbidity and highly nutritive as ammonia and nitrate contents were highly increased. In E. coli free vermiaqua, BOD5 loads were also reduced by 91% Almost all vermiaqua treated root germinations were 'accelerated' whereas all wastewater treated root germinations were 'retarded' The highest number of germinated roots was counted at 10 5 concentration of vermiaqua, whereas at the same concentration of wastewater no germination was observed. Many types of chromosomal abnormalities were observed at metaphase and anaphase stages of wastewater treated roots, whereas the single type of chromosomal abnormality was observed at anaphase stage of vermiaqua treated roots.ConclusionsEarthworms upgraded the performance of fabricated systems having integrated methods (biological, chemical and physical) of wastewater purification. Morphological and cytological studies revealed vermiaqua highly promoted the root germination without any chromosomal abnormalities.
Variability in reproductive traits in Jatropha curcas L. accessions during early developmental stages under warm subtropical conditions
Year: 2015

Variability in floral, fruit, and seed characteristics, and oil content of 15 accession of Jatropha curcas during early development were assessed during two flowering periods in south Florida subtropical climate. The two flowering periods had leaf flushing in March. Field evaluation using 18 quantitative traits showed significant variation among accessions. The number of female flowers and female male flower ratio ranged from 1 to 15 and 1 8.8 to 1 67.8, respectively. Fruit set by natural pollination was 89 and 66% during the first (1st) and second (2nd) flowering periods, respectively. A higher number of female type inflorescences were observed during summer. There were significant differences in seed traits, except for number of seeds per fruit. Accession TREC 31 had the highest individual seed dry weight and 100 seed weight (0.83 g and 79.7 g, respectively) The oil content varied from 19.30% to 35.62% Seed dry weight had positive correlation with seed fresh weight, seed length, seed thickness, seed width, and 100 seed weight, but negative correlation with oil content. Based on the cluster analysis using 15 morphological traits, jatropha accessions were grouped into five main clusters and accessions from different geographic regions grouped together in a cluster. Principal component analyses (PCA) revealed morphological variation. The first three components explained 73.5% of the total variation and seed dry weight, 100 seed weight, total flowers per inflorescence, male flowers per inflorescence and fruit set can be used to distinguish accessions. The PCA also indicated that flowering traits were more influenced by seed origin while seed traits were affected by flowering spans. Although evaluations were performed in plants during the juvenile phase, accessions TREC 31 and TREC 55 had superior averages for almost all characters evaluated. These results provide a preliminary assessment of the high variability in jatropha accessions evaluated and their potential for use in breeding and genetic improvement programs.
Dynamic Network Analysis of Negative Emotions and DSM 5 Posttraumatic Stress Disorder Symptom Clusters During Conflict.
Venue: Journal of traumatic stress
Year: 2019

Investigating dynamic associations between specific negative emotions and PTSD symptom clusters may provide novel insights into the ways in which PTSD symptoms interact with, emerge from, or are reinforced by negative emotions. The present study estimated the associations among negative emotions and the four DSM 5 PTSD symptom clusters (intrusions, avoidance, negative alterations in cognitions and mood [NACM] and arousal) in a sample of Israeli civilians (n 96) during the Israel Gaza War of July August 2014. Data were collected using experience sampling methodology, with participants queried via smartphone about PTSD symptoms and negative emotions twice a day for 30 days. We used a multilevel vector auto regression model to estimate temporal and contemporaneous temporal networks. Contrary to our hypothesis, in the temporal network, PTSD symptom clusters were more predictive of negative emotions than vice versa, with arousal emerging as the strongest predictor that negative emotions would be reported at the next measurement point; fear and sadness were also strong predictors of PTSD symptom clusters. In the contemporaneous network, negative emotions exhibited the strongest associations with the NACM and arousal PTSD symptom clusters. The negative emotions of sadness, stress, fear, and loneliness had the strongest associations to the PTSD symptom clusters. Our findings suggest that arousal has strong associations to both PTSD symptoms and negative emotions during ongoing trauma and highlights the potentially relevant role of arousal for future investigations in primary or early interventions.
Mechanical responses of Ti 6Al 4V cuboctahedral truss lattice structures
Year: 2020

Ti 6Al 4V cuboctahedral truss lattice structures were manufactured via a combined approach of snap fitting and vacuum brazing. By varying the strut length l from 7.7 to 22 mm, structures of relative densities in the 1.5 7.5% range were fabricated and mechanically tested in compression. Lattice collapse mode transformed from elastic to inelastic truss buckling at a relative density 2.5% corresponding to a strut aspect ratio t l 0.09. The mechanical properties are found to be sample size dependent, and are significantly knocked down in small sized specimens by the soft edges. A low nodal connectivity Z 8 of the cuboctahedral truss topology makes it less efficient to attain the maximum mechanical performance, and nodal fractures preceded the attainment of numerically anticipated lattice peak strength. Nonetheless, mechanical properties of cuboctahedral structures are competitive with existing topologies and materials, and the full potential performance could be achieved in structures with large numbers of in plane cells.
Effects of shadow banking on bank risks from the view of capital adequacy
Venue: International Review of Economics Finance
Year: 2019

This study examines two issues. First, we propose that a bank that engages in shadow banking tends to take considerable risks, and we call this effect the risk taking hypothesis. Second, we examine whether good corporate governance can enhance or mitigate this effect of shadow banking on risk taking. Our sample consists of 59 Chinese banks during 2010 2016. We represent shadow banking with three trust beneficiary rights: financial assets purchased under resale agreements, financial assets available for sale, and investment securities received. Our results support the risk taking hypothesis and the tendency of good governance to significantly reduce the effect of shadow banking on risk taking.
Combating Health Disparities in Cambodian American Communities: A CBPR Approach to Building Community Capacity
Venue: Progress in community health partnerships research, education, and action
Year: 2017

Cambodian Americans have higher rates of health problems compared with the general U.S. population. A relatively modest community capacity for collecting data contributes to these disparities. To (1) further develop the Cambodian American community's capacity to design and conduct health research meaningful to their community via a community based participatory research (CBPR) approach, (2) train and deploy bilingual community health workers (CHWs) to gather health related data from their communities using mobile technology, and (3) measure the feasibility and effectiveness of our efforts. A CBPR approach was used to engage leaders of Cambodian American communities in six states to identify their research needs, develop a short community health survey administered by CHWs, and conduct the survey using iPads programmed in Khmer spoken language format. Administrative logs and surveys of CHWs and leaders measured feasibility and effectiveness of the project. CHWs, leaders, and community members reported largely positive experiences with the community health survey, despite poor/inconsistent Internet connectivity. The institutional capacity of Cambodian American community based organizations to collect health related data in their own communities was strengthened. Our efforts proved to be both feasible and effective. The use of mobile technology with spoken format can be a valuable tool in accessing input from vulnerable community members, including persons who may not be literate in any language. Trained CHWs, backed by dedicated and experienced community leaders, are an asset to their communities. Together, they are uniquely placed to make important contributions to the well being of their community.