nils-herrmann/clean_scirepeval huggingface dataset:
Aplikasi Pengajuan Pendaftaran Kegiatan di Pusat Data dan Informasi Kementerian Kesehatan Republik Indonesia
Year: 2019

Aplikasi Pengajuan Pendaftaran Kegiatan adalah sebuah aplikasi yang digunakan untuk membuat pendaftaran kegiatan staff satuan kerja/inker di lingkungan Kementerian Kesehatan Republik Indonesia. Aplikasi ini dibangun untuk mempermudah staff satuan kerja/inker dalam pendaftaran kegiatan hosting, collocoation, update data hosting upgrade space hosting dan juga laporan penyerahan hosting, karena proses yang berlangsung saat ini masih menggunakan Microsoft Word, data harus terintegrasi dengan baik. Aplikasi ini bertujuan untuk memudahkan kepala bagian dalam proses approval pengajuan kegiatan yang telah diajukan oleh staff satuan kerja/inker. Aplikasi ini dibangun dengan menggunakan Bahasa PHP, berbasis website dan dengan framework CodeIgniter. Proses pembangunan aplikasi menggunakan metode SDLC Waterfall. Hasil akhir dari plikasi ini dapat digunakan dan diterapkan pada sistem Informasi Kementerian Kesehatan Republik Indonesia bagian Pusat Data dan Informasi. Hosting, Collocation, Kegiatan, Pengajuan, Approval.
Endless paces of degeneration applying comparative genomics to study evolution's moulding of longevity
Venue: EMBO reports
Year: 2013

Why can mice not live more than five years and dogs not more than 30, yet bats can live over 40 years and humans over a century? Differences in longevity between closely related species are one of the greatest mysteries in biology, and identifying the processes responsible could ultimately presage the development of therapies against a multitude of age related diseases. The variation in mammalian longevity must have a genomic basis, with recent genome sequencing efforts opening up exciting opportunities to decipher it; some promising results are beginning to emerge. Analysis of two bat genomes revealed that a high proportion of genes in the DNA damage checkpoint DNA repair pathway, including ATM TP53 RAD50 and KU80 are under selection in bats  This finding is exciting because these genes have been directly associated with ageing in model systems and, therefore, it points towards a potential role for
Clinical Application of Overlapping Confidence Intervals for Monitoring Changes in Serial Clinical Chemistry Test Results
Venue: Annals of laboratory medicine
Year: 2020

Interpretation of changes in serial laboratory results is necessary for both clinicians and laboratories; however, setting decision limits is not easy. Although the reference change value (RCV) has been widely used for auto verification, it has limitations in clinical settings. We introduce the concept of overlapping confidence intervals (CIs) to determine whether the changes are statistically significant in clinical chemistry laboratory test results.  In total, 1,202,096 paired results for 33 analytes routinely tested in our clinical chemistry laboratory were analyzed. The distributions of delta% absolute values and cut off values for certain percentiles were calculated. The CIs for each analyte were set based on biological variation, and data were analyzed at various confidence levels. Additionally, we analyzed the data using RCVs and compared their clinical utility.  Most analytes had low indexes of individuality with large inter individual variability. The 97.5th percentile cut offs for each analyte were much larger than conventional RCVs. The percentages of results exceeding RCV95% and RCV99% corresponded to those with no overlap at the 83.4% and 93.2% confidence levels, respectively.  The use of overlapping CIs in serial clinical chemistry test results can overcome the limitations of existing RCVs and replace them, especially for analytes with large intra individual variation.
Mean cortical curvature reflects cytoarchitecture restructuring in mild traumatic brain injury
Venue: NeuroImage: Clinical
Year: 2016

In the United States alone, the number of persons living with the enduring consequences of traumatic brain injuries is estimated to be between 3.2 and 5 million. This number does not include individuals serving in the United States military or seeking care at Veterans Affairs hospitals. The importance of understanding the neurobiological consequences of mild traumatic brain injury (mTBI) has increased with the return of veterans from conflicts overseas, many of who have suffered this type of brain injury. However, identifying the neuroanatomical regions most affected by mTBI continues to prove challenging. The aim of this study was to assess the use of mean cortical curvature as a potential indicator of progressive tissue loss in a cross sectional sample of 54 veterans with mTBI compared to 31 controls evaluated with MRI. It was hypothesized that mean cortical curvature would be increased in veterans with mTBI, relative to controls, due in part to cortical restructuring related to tissue volume loss. Mean cortical curvature was assessed in 60 bilateral regions (31 sulcal, 29 gyral) Of the 120 regions investigated, nearly 50% demonstrated significantly increased mean cortical curvature in mTBI relative to controls with 25% remaining significant following multiple comparison correction (all, pFDR .05) These differences were most prominent in deep gray matter regions of the cortex. Additionally, significant relationships were found between mean cortical curvature and gray and white matter volumes (all, p .05) These findings suggest potentially unique patterns of atrophy by region and indicate that changes in brain microstructure due to mTBI are sensitive to measures of mean curvature.
Neural speech recognition: continuous phoneme decoding using spatiotemporal representations of human cortical activity.
Venue: Journal of neural engineering
Year: 2016

The superior temporal gyrus (STG) and neighboring brain regions play a key role in human language processing. Previous studies have attempted to reconstruct speech information from brain activity in the STG, but few of them incorporate the probabilistic framework and engineering methodology used in modern speech recognition systems. In this work, we describe the initial efforts toward the design of a neural speech recognition (NSR) system that performs continuous phoneme recognition on English stimuli with arbitrary vocabulary sizes using the high gamma band power of local field potentials in the STG and neighboring cortical areas obtained via electrocorticography.  The system implements a Viterbi decoder that incorporates phoneme likelihood estimates from a linear discriminant analysis model and transition probabilities from an n gram phonemic language model. Grid searches were used in an attempt to determine optimal parameterizations of the feature vectors and Viterbi decoder.  The performance of the system was significantly improved by using spatiotemporal representations of the neural activity (as opposed to purely spatial representations) and by including language modeling and Viterbi decoding in the NSR system.  These results emphasize the importance of modeling the temporal dynamics of neural responses when analyzing their variations with respect to varying stimuli and demonstrate that speech recognition techniques can be successfully leveraged when decoding speech from neural signals. Guided by the results detailed in this work, further development of the NSR system could have applications in the fields of automatic speech recognition and neural prosthetics.
Total phenolic and total flavonoid content of sugar cane juice and their potency as alpha amylase inhibitor and anti COVID 19
Year: 2021

Diabetes Mellitus (DM) and COVID 19 diseases are still global problems. One of the causes of DM, mainly type 2 is unhealthy eating habits, including white sugar, which contains almost no active compounds except sucrose. The active compounds in sugarcane juice such as ferulic acid, gallic acid, 4 Hydroxy benzoate acid, and vanillic acid, which are suspected besides alpha amylase inhibitors, also have potential as anti COVID 19. The purpose of this research is to extract secondary metabolites from sugarcane juice, determine TPC and TFC, and to know in silico activity of the active compounds in sugarcane juice as an alpha amylase inhibitor and binding position to the active site of the spike protein. The results have shown that TPC and TFC in sugarcane juice are 0.5501% and 0.4480% The in silico analysis has proven that the ferulic acid compound is bonded to the alpha amylase binding site as acarbose did. Gallic acid, 4 hydroxy benzoic acid, and vanillic acid compounds are bonded to RBD of S protein COVID 19 as chloroquine did, with various binding affinity. These results indicate that phenolic and flavonoids in sugarcane juice have the potential as an alpha amylase inhibitor and anti COVID 19.
MDCube: a high performance network structure for modular data center interconnection
Venue: CoNEXT '09
Year: 2009

Shipping container based data centers have been introduced as building blocks for constructing mega data centers. However, it is a challenge on how to interconnect those containers together with reasonable cost and cabling complexity, due to the fact that a mega data center can have hundreds or even thousands of containers and the aggregate bandwidth among containers can easily reach tera bit per second. As a new inner container server centric network architecture,  interconnects thousands of servers inside a container and provides high bandwidth support for typical traffic patterns. It naturally serves as a building block for mega data center. In this paper, we propose MDCube, a high performance interconnection structure to scale BCube based containers to mega data centers. MDCube uses the high speed uplink interfaces of the commodity switches in BCube containers to build the inter container structure, reducing the cabling complexity greatly. MDCube puts its inter and inner container routing intelligences solely into servers to handle load balance and fault tolerance, thus directly leverages commodity instead of high end switches to scale. Through analysis, we prove that MDCube has low diameter and high capacity. Both simulations and experiments in our testbed demonstrate the fault tolerance and high network capacity of MDCube.
Soziale Medien als Mittel der Produktgestaltung (Co Creation)
Year: 2014

Soziale Medien befahigen Konsumenten Inhalte im Internet interaktiv zu gestalten und ermoglichen einen Paradigmenwechsel in der Konsumenten Produzenten Beziehung. Der klassische Wertschopfungsprozess sieht eine klare Rollentrennung von Konsument und Produzent vor. Unternehmen ubernehmen Aufgaben wie Forschung, Entwicklung, Marketing und Vertrieb und treten erst beim Warenaustausch mit dem Kunden in Kontakt. Soziale Medien erlauben die Integration von Konsumenten in den Wertschopfungsprozess und fuhren zu einer Aufweichung der klassischen Rollenteilung. Eine Vielzahl von Konsumenten kann durch Online Plattformen in unterschiedlichen Phasen der Wertschopfung eingebunden werden. Klassische hierarchische und marktbasierte Koordinationsmechanismen werden durch Prinzipien der Selbstmotivation und Selbstorganisation abgelost. Die weitgreifende Interaktion und Partizipation ermoglicht nicht nur Produktinnovationen, sondern kann auch die Kundenbindung steigern. Viele Unternehmen wie z.B. McDonald's, Dell und Nespresso setzen Soziale Medien zur interaktiven Produktgestaltung ein. Der erfolgreiche Einsatz von Sozialen Medien zur Produktgestaltung stellt jedoch eine grose Herausforderung dar. Zahlreiche Instrumente wie z.B. Ideenwettbewerbe oder Konfigurationstools konnen in unterschiedlichen Phasen der Wertschopfung unter verschiedenen Rahmenbedingungen verwendet werden. Das Resultat interaktiver Produktgestaltung ist schwer vorhersehbar. Die interagierende Masse an Konsumenten lasst sich kaum kontrollieren und ist unter Umstanden in der Lage, Image und Absatz zu gefahrden. Der Beitrag stellt Chancen und Risiken des Einsatzes sozialer Medien zur Produktgestaltung gegenuber und zeigt Erfolgsfaktoren bei der Ausgestaltung verschiedener Instrumente auf. Hierbei werden jeweils Erkenntnisse aus der Wissenschaft und Fallbeispiele aus der Unternehmenspraxis prasentiert.
Ascorbic acid and reactive oxygen species are involved in the inhibition of seed germination by abscisic acid in rice seeds
Venue: Journal of experimental botany
Year: 2012

The antagonism between abscisic acid (ABA) and gibberellin (GA) plays a key role in controlling seed germination, but the mechanism of antagonism during this process is not known. The possible links among ABA, reactive oxygen species (ROS) ascorbic acid (ASC) and GA during rice seed germination were investigated. Unlike in non seed tissues where ROS production is increased by ABA, ABA reduced ROS production in imbibed rice seeds, especially in the embryo region. Such reduced ROS also led to an inhibition of ASC production. GA accumulation was also suppressed by a reduced ROS and ASC level, which was indicated by the inhibited expression of GA biosynthesis genes, amylase genes, and enzyme activity. Application of exogenous ASC can partially rescue seed germination from ABA treatment. Production of ASC, which acts as a substrate in GA biosynthesis, was significantly inhibited by lycorine which thus suppressed the accumulation of GA. Consequently, expression of GA biosynthesis genes was suppressed by the low levels of ROS and ASC in ABA treated seeds. It can be concluded that ABA regulates seed germination in multiple dimensions. ROS and ASC are involved in its inhibition of GA biosynthesis.
The Experience of Alienation in Toni Morrison's Work: Man's Fragmentation and Concomitant Distortion
Year: 2017

The question of alienation has always been a pervasive theme in the history of modern thought, and it occupies a considerable place in contemporary work. Literature in general, and fiction in particular, raise this issue to reveal its influence on human beings and communities. Novelists have been trying to unravel its complexities and concomitant consequences. The paper aims to explore the experience of alienation through depicting the issue not as a purely racial reality, or something restricted to the colour of the skin or gender of the victim. It is rather presented as a distressing state which cripples the victims and makes them susceptible captives of the dominant forces. In the selected novels, Toni Morrison has delved deep into the experience of alienation through her male and female characters, showing the different forms of this experience. The present research investigates Morrison's portrayal of the issue from an African American prospect. References will be made to novels such as Tar Baby, Sula, The Bluest Eye, Song of Solomon, and Beloved.
Embracing carbon neutral electricity and transportation sectors in Cyprus
Year: 2021

From the energy standpoint Cyprus is unique because the island relies on oil fired power generation while the national electricity grid is isolated. Yet short driving distances render the country a testbed for a full electric vehicle fleet. Based on EU climate goals, passenger vehicles and buses were considered 100% electric by 2050. Spanning between 2018 and 2050, herein we present the future electricity needs and vehicle fleet size, which currently account for 77% of the island's emissions. In parallel, four distinct scenarios, namely, the Least Cost (LCSc) the Business As Usual (BAU) the Carbon Capture and Storage (CCSc) and the Renewables (RESc) are presented. Weekly hourly profiles of electricity production and consumption were deduced during the winter and summer seasons. Passenger vehicle to grid units and desalination plants helped estimate the grid's electrical load. Projections demonstrated that the RESc in 2050 yields the costliest electricity (0.115EUR/kWh) accompanied by the highest electricity losses (40% A domestic battery storage of 5,600MWh is required, whereas Europe's current battery capacity is 3,400MWh. In the context of EC's goals, the BAU and LCSc cases fail to meet the 2degC emissions threshold while the CCSc abides with the preceding target. Concluding, RESc attains full decarbonisation.
Marketing Concept The St. Gallen Management Approach
Year: 2015

This book presents marketing and business processes as an integral part of the St.Gallen Management Model. It provices a tight introduction into the field of marketing and puts the added value in the center of a market oriented management approach. The book addresses relevant topics such as market analysis, marketing planning marketing strategy, positioning, application of marketing tools. product design, price, distribution and communication policy, service provision, innovation and controlling processes. This book aims at students in the first year as well as at practitioners who wants to obtain a quick overview of this field.
Sentiment Analysis of German Twitter
Venue: ArXiv
Year: 2019

This thesis explores the ways by how people express their opinions on German Twitter, examines current approaches to automatic mining of these feelings, and proposes novel methods, which outperform state of the art techniques. For this purpose, I introduce a new corpus of German tweets that have been manually annotated with sentiments, their targets and holders, as well as polar terms and their contextual modifiers. Using these data, I explore four major areas of sentiment research: (i) generation of sentiment lexicons, (ii) fine grained opinion mining, (iii) message level polarity classification, and (iv) discourse aware sentiment analysis. In the first task, I compare three popular groups of lexicon generation methods: dictionary corpus and word embedding based ones, finding that dictionary based systems generally yield better lexicons than the last two groups. Apart from this, I propose a linear projection algorithm, whose results surpass many existing automatic lexicons. Afterwords, in the second task, I examine two common approaches to automatic prediction of sentiments, sources, and targets: conditional random fields and recurrent neural networks, obtaining higher scores with the former model and improving these results even further by redefining the structure of CRF graphs. When dealing with message level polarity classification, I juxtapose three major sentiment paradigms: lexicon machine learning and deep learning based systems, and try to unite the first and last of these groups by introducing a bidirectional neural network with lexicon based attention. Finally, in order to make the new classifier aware of discourse structure, I let it separately analyze the elementary discourse units of each microblog and infer the overall polarity of a message from the scores of its EDUs with the help of two new approaches: latent marginalized CRFs and Recursive Dirichlet Process.
Pattern of recurrence after CyberKnife stereotactic body radiotherapy for peripheral early non small cell lung cancer.
Venue: Journal of thoracic disease
Year: 2019

The treatment efficacy after CyberKnife stereotactic body radiotherapy (SBRT) have not been adequately addressed. The purpose of this study was to investigate pattern of recurrence according to irradiation field after CyberKnife SBRT for early stage non small cell lung cancer (NSCLC)  This retrospective study included patients with peripheral cT1/2N0M0 NSCLC that was treated with SBRT using a CyberKnife between May 2013 and March 2016 at single institute and followed up by more than two imaging examinations. Both operable and inoperable patients were included. Overall survival (OS) and progression free survival (PFS) curves were estimated using the Kaplan Meier method with 95% confidence intervals (CI) Cumulative incidence curves of recurrence were calculated and compared using the Gray's test.  Total 71 patients were included and analyzed in this study. The median follow up period for surviving patients was 34 months (range, 7 64 months) The 2 year OS and PFS rate were 93% (95% CI: 83 97% and 77% (95% CI: 65 86% respectively. The 2 year cumulative incidence rate of infield recurrence and out of field recurrence were 6% (95% CI: 2 14% and 17% (95% CI: 9 27% respectively. Gross tumor volume (GTV) =9 mL and diagnosis to treatment interval (DTI) =90 days were significantly associated with infield recurrence (P<0.001 and P=0.007) and epidermal growth factor receptor (EGFR) mutation was significantly associated with out of field recurrence (P=0.014)  Treatment efficacy after CyberKnife SBRT for peripheral early stage NSCLC was identical to previous conventional linac based SBRT reports. With short follow up period, it was found that GTV and DTI were the significant predictive factor of infield recurrence, and EGFR mutation was the significant predictive factor of out of field recurrence.
Intereye Comparison of Focal Lamina Cribrosa Defect in Normal Tension Glaucoma Patients with Asymmetric Visual Field Loss
Venue: Ophthalmic Research
Year: 2020

To evaluate the association of focal lamina cribrosa (LC) defect with asymmetric visual field (VF) loss in normal tension glaucoma (NTG) through intereye comparisons.  Paired eyes were divided into better and worse eyes according to the mean deviation (MD) and ocular parameters were compared between them. Furthermore, patients in the asymmetric group were classified as subgroup A (one eye with LC defect and the fellow one without) subgroup B (both eyes without LC defect) and subgroup C (both eyes with LC defect) Generalized estimation equation approach was used to evaluate the association between ocular parameters and asymmetric VF.  A total of 140 eyes of 70 NTG patients were included in the asymmetric group. LC defects were more common in better eyes than that in worse eyes (27/70 [38.57% vs. 10/70 [14.29% p 0.001) and all eyes with LC defect had myopia. Multivariate analysis revealed that the presence of LC defect was significantly associated with better eyes in the asymmetric group (odds ratio, 0.27; p 0.001) For subgroup A, eyes with LC defects exhibited lower peak IOP (p 0.011) and lower mean IOP (p 0.018) than the fellow eyes without. In addition, longer AL (p 0.025) and larger tilt ratio (p 0.032) were found in eyes with LC defects. For subgroup B without LC defects, larger tilt ratio was shown to be a risk factor for VF loss (odds ratio, 6.13; p 0.001) There was no significant difference of binocular parameters except for MD (p 0.001) in subgroup C.  LC defects in myopia were suggested to be associated with better eyes in NTG with asymmetric VF loss. However, in patients without LC defect, larger tilt ratio was a risk factor for VF defect. There might be different pathological mechanisms in asymmetric VF loss for different NTG subtypes.