nils-herrmann/clean_scirepeval huggingface dataset:
The potential of sedimentary ancient DNA for reconstructing past sea ice evolution
Venue: The ISME Journal
Year: 2019

Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA) as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea ice associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.
Peer group normalization and urine to blood context in steroid metabolomics: The case of CAH and obesity
Venue: Steroids
Year: 2014

Traditional interpretation of GC MS output involved the semi quantitative estimation of outstanding low or high specific metabolites and the ratio between metabolites. Here, we utilize a systems biology approach to steroid metabolomics of a complex steroid related disorder, using an all inclusive analysis of the steroidal pathway in the form of a subject steroidal fingerprint and disease signature, providing novel methods of normalization and visualization. The study compares 324 normal children to pure enzymatic deficiency in 27 untreated 21 hydroxylase CAH patients and to complex disease in 70 children with obesity. Steroid profiles were created by quantitative data generated by GC MS analyses. A novel peer group normalization method defined each individual subject's control group in a multi dimensional space of metadata parameters. Classical steroid pathway visualization was enhanced by adding urinary end product sub nodes and by color coding of semi quantitative metabolic concentrations and enzymatic activities. Unbiased automated data analysis confirmed the common knowledge for CAH the inferred 17 hydroxyprogesterone was up regulated and the inferred 21 hydroxylase enzyme activity was down regulated. In childhood obesity, we observe a general decrease of both glucocorticoid and mineralocorticoid metabolites, increased androgens, up regulation of 17,20 lyase, 17 OHase and 11b HSD1 activity and down regulation of 21 OHase enzymatic activity. Our study proved novel normalization and visualization techniques are to be useful in identifying subject fingerprint and disease signature in enzymatic deficiency and insufficiency, while demonstrating hypothesis generation in a complex disease such as childhood obesity.
Transliteration for Cross Lingual Morphological Inflection
Venue: SIGMORPHON
Year: 2020

Cross lingual transfer between typologically related languages has been proven successful for the task of morphological inflection. However, if the languages do not share the same script, current methods yield more modest improvements. We explore the use of transliteration between related languages, as well as grapheme to phoneme conversion, as data preprocessing methods in order to alleviate this issue. We experimented with several diverse language pairs, finding that in most cases transliterating the transfer language data into the target one leads to accuracy improvements, even up to 9 percentage points. Converting both languages into a shared space like the International Phonetic Alphabet or the Latin alphabet is also beneficial, leading to improvements of up to 16 percentage points.
Discretionary Budget Authority by Subfunction: An Overview
Year: 2012

President Obama's FY2013 budget submission was released on February 13, 2012. This report provides a graphical overview of historical trends in discretionary budget authority (BA) from FY1976 through FY2011, enacted levels for FY2012 spending, and the levels consistent with the President's proposals for FY2013 through FY2017. Spending caps and budget enforcement mechanisms established in the Budget Control Act (BCA) of 2011 will probably strongly affect the FY2013 budget cycle. This report may provide a starting point for discussions about spending trends and federal priorities, but it does not attempt to explain spending patterns in each policy area.
Association of Rotavirus Vaccination With the Incidence of Type 1 Diabetes in Children
Venue: JAMA pediatrics
Year: 2019

Rotavirus (RV) infection has been associated with the development of type 1 diabetes (T1D) in  Rotavirus infection triggers pancreatic apoptosis in mice, and RV peptides display molecular mimicry with T cell epitopes in pancreatic b cell autoantigens.2 We hypothesized that if natural infection with RV was a causative factor in T1D, then RV vaccination would decrease the incidence of disease over time. Therefore, using publicly available data, we examined the incidence of T1D in Australian children before and after the oral RV vaccine was introduced to the Australian National Immunisation Program in 2007.
Exploring Student Teachers' Views on ePortfolios as an Empowering Tool to Enhance Self Directed Learning in an Online Teacher Education Course
Year: 2017

This paper explores Economics student teachers' views on ePortfolios as an empowering tool to enhance self directed learning in an online teacher education course. An interpretive phenomenological research approach was employed for data collection and a purposive convenient sampling technique was selected to collect data. Only Postgraduate Certificate of Education (PGCE) and Batchelor of Education (BEd) Senior Phase/Further Education and Training Economics Subject Methodology (SDEC00N) student teachers registered on myUnisa for the modules were targeted. Multiple sections from the ePortfolios that had been considered for the purpose of this study were taken from their creative writing assignments, a research projects, lesson plans, reflective journal entries, podcasts, blog postings. Data were collected and analysed on a weekly basis to create a plethora of information. Student teachers felt that they were empowered with different subject content knowledge, technological pedagogical content knowledge (TPCK) and other technologies, student centred methods and techniques through the ePortfolio project.
Grid tied photovoltaic system based on PSO MPPT technique with active power line conditioning
Year: 2016

This study presents a single phase grid tied photovoltaic (PV) system based on a global maximum power point tracking (MPPT) technique, which is performed by means of the particle swarm optimisation (PSO) method. The PSO based MPPT technique is employed to solve problems related to mismatching phenomena, such as partial shading, in which the PV arrays are commonly submitted. Considering the search of the global maximum power point under partial shading, the effectiveness of the PSO based MPPT technique is highlighted when compared with the well known perturb and observe MPPT technique, since both the mentioned MPPT techniques are used to determine the dc bus voltage reference to ensure a proper grid tied inverter operation. A current generator algorithm based on a synchronous reference frame is proposed, which operates in conjunction with a dc bus controller and MPPT algorithms, computing the reference current of the grid tied inverter. In addition, the current generator controls the energy processed by the PV system to avoid over power rating of the grid tied inverter, since the active power injection into the grid, reactive power compensation and harmonic currents suppression are carried out simultaneously. The performance and feasibility of the grid tied PV system are evaluated by means of simulation and experimental results.
PROSES PENGOLAHAN IKAN BANDENG (Chanos chanos) SEBAGAI BAHAN DASAR PEMBUATAN NUGGET BANDENG DI CV. FANIA FOOD, YOGYAKARTA
Year: 2017

Ikan bandeng merupakan komoditas yang cukup melimpah di perairan Indonesia dan tergolong sumber daya perairan yang paling banyak diminati. Ikan bandeng yang memiliki kandungan gizi yang baik, yaitu tinggi protein dan rendah lemak, sehingga dapat dimanfaatkan sebagai produk makanan yang sesuai dengan kelayakan dan kebutuhan gizi protein masyarakat Indonesia. Salah satu alternatif bentuk pengolahan yang paling banyak berkembang di kalangan masyarakat adalah pembuatan produk nugget, dan nugget dari ikan bandeng merupakan salah satu dari diversifikasi produk perikanan yang layak untuk dikonsumsi masyarakat Indonesia. Kelemahan ikan bandeng adalah memiliki duri yang banyak dan ikan mengalami proses pembusukan yang cepat sehingga perlu adanya penanganan dan pengolahan daging ikan secara baik dan benar, mulai dari penanganan bahan baku ikan hingga pengemasan nugget ikan bandeng. Praktek Kerja Lapang dilaksanakan di Jalan Semangu KG 1 No.16 RT.3 RW.1 Gedongkuning Rejowinangun, Kecamatan Kotagede, Kota Yogyakarta, Daerah Istimewa Yogyakarta pada tanggal 23 Januari hingga 22 Februari 2017. Metode kerja yang digunakan adalah metode deskriptif dengan pengambilan datayang meliputi data primer dan data sekunder. Pengambilan data dilakukan dengan cara observasi, wawancara, partisipasi aktif, sedangkan perolehan data sekunder dilakukan dengan membaca studi pustaka. Tujuan dari Praktek Kerja Lapang (PKL) ini adalah untuk mengetahui proses pengolahan ikan bandeng sebagai bahan dasar pembuatan nugget bandeng di CV.  Food, Yogyakarta.
LinkNet: 2D 3D linked multi modal network for online semantic segmentation of RGB D videos
Venue: Comput. Graph.
Year: 2021

This paper proposes LinkNet, a 2D 3D linked multi modal network served for online semantic segmentation of RGB D videos, which is essential for real time applications such as robot navigation. Existing methods for RGB D semantic segmentation usually work in the regular image domain, which allows efficient processing using convolutional neural networks (CNNs) However, RGB D videos are captured from a 3D scene, and different frames can contain useful information of the same local region from different views. Working solely in the image domain fails to utilize such crucial information. Our novel approach is based on joint 2D and 3D analysis. The online process is realized simultaneously with 3D scene reconstruction, from which we set up 2D 3D links between continuous RGB D frames and 3D point cloud. We combine image color and view insensitive geometric features generated from the 3D point cloud for multi modal semantic feature learning. Our LinkNet further uses a recurrent neural network (RNN) module to dynamically maintain the hidden semantic states during 3D fusion, and refines the voxel based labeling results. The experimental results on SceneNet  and ScanNet  demonstrate that the semantic segmentation results of our framework are stable and effective.
Social evolution and genetic interactions in the short and long term.
Venue: Theoretical population biology
Year: 2015

The evolution of social traits remains one of the most fascinating and feisty topics in evolutionary biology even after half a century of theoretical research. W.D. Hamilton shaped much of the field initially with his 1964 papers that laid out the foundation for understanding the effect of genetic relatedness on the evolution of social behavior. Early theoretical investigations revealed two critical assumptions required for Hamilton's rule to hold in dynamical models: weak selection and additive genetic interactions. However, only recently have analytical approaches from population genetics and evolutionary game theory developed sufficiently so that social evolution can be studied under the joint action of selection, mutation, and genetic drift. We review how these approaches suggest two timescales for evolution under weak mutation: (i) a short term timescale where evolution occurs between a finite set of alleles, and (ii) a long term timescale where a continuum of alleles are possible and populations evolve continuously from one monomorphic trait to another. We show how Hamilton's rule emerges from the short term analysis under additivity and how non additive genetic interactions can be accounted for more generally. This short term approach reproduces, synthesizes, and generalizes many previous results including the one third law from evolutionary game theory and risk dominance from economic game theory. Using the long term approach, we illustrate how trait evolution can be described with a diffusion equation that is a stochastic analogue of the canonical equation of adaptive dynamics. Peaks in the stationary distribution of the diffusion capture classic notions of convergence stability from evolutionary game theory and generally depend on the additive genetic interactions inherent in Hamilton's rule. Surprisingly, the peaks of the long term stationary distribution can predict the effects of simple kinds of non additive interactions. Additionally, the peaks capture both weak and strong effects of social payoffs in a manner difficult to replicate with the short term approach. Together, the results from the short and long term approaches suggest both how Hamilton's insight may be robust in unexpected ways and how current analytical approaches can expand our understanding of social evolution far beyond Hamilton's original work.
Diagnostic Value of Serum hsa mir 92a in Patients with Cervical Cancer.
Venue: Clinical laboratory
Year: 2017

Hsa mir 92a acts as an onco miRNA and may contribute to the progression and invasion of cervical cancer, which is a common malignant tumor in women worldwide. The objective of the present study was to evaluate whether serum hsa mir 92a could serve as a diagnostic biomarker for cervical cancer patients.  The expression levels of hsa mir 92a were analyzed in the serum of patients with CIN I, CIN II, CIN III, cervical cancer Ia IIa and compared with those of the control group samples. The receiver operating characteristic (ROC) curve was used to evaluate the diagnostic significance of cervical cancer.  It was found that the expression of hsa miR 92a in the serum of individuals with CIN or cervical cancer was significantly higher than that in healthy volunteers (p 0.01) The expression of hsa miR 92a was higher in the serum of patients with advanced stage and cervical cancer than those with early stage. ROC analysis revealed that the cutoff value of hsa mir 92a was 1.52 for the diagnosis of CIN and cervical cancer. The sensitivity and specificity were 69.6% and 80.4% respectively, and an area under the curve (AUC) was 0.83.
Memory chip design using cadence
Year: 2014

In this paper an effort is made to design 16 bit SRAM memory array on 180nm technology. For high speed memory applications such as cache, a SRAM is often used. Access time, speed, and power consumption are the three key parameters for an SRAM memory design (SRAM) The integrated SRAM is operated with analog input voltage of 0 to 1.8v. The 16 bit SRAM memory has been designed, implemented &analysed in standard UMC180nm technology library using Cadence tool.We alsoanalyse the read and write operation of the designed memory cell.
Social media use by government: from the routine to the critical
Venue: dg.o '11
Year: 2011

Social media (i.e. Twitter, Facebook, Flickr, YouTube) and other services with user generated content have made a staggering amount of information (and misinformation) available. Government officials seek to leverage these resources to improve services and communication with citizens. Yet, the sheer volume of social data streams generates substantial noise that must be filtered. Nonetheless, potential exists to identify issues in real time, such that emergency management can monitor and respond to issues concerning public safety. By detecting meaningful patterns and trends in the stream of messages and information flow, events can be identified as spikes in activity, while meaning can be deciphered through changes in content. This paper presents findings from a pilot study we conducted between June and December 2010 with government officials in Arlington, Virginia (and the greater National Capitol Region around Washington, DC) with a view to understanding the use of social media by government officials as well as community organizations, businesses and the public. We are especially interested in understanding social media use in crisis situations (whether severe or fairly common, such as traffic or weather crises)
Diversity Sensitive Conditional Generative Adversarial Networks
Venue: ICLR
Year: 2019

We propose a simple yet highly effective method that addresses the mode collapse problem in the Conditional Generative Adversarial Network (cGAN) Although conditional distributions are multi modal (i.e. having many modes) in practice, most cGAN approaches tend to learn an overly simplified distribution where an input is always mapped to a single output regardless of variations in latent code. To address such issue, we propose to explicitly regularize the generator to produce diverse outputs depending on latent codes. The proposed regularization is simple, general, and can be easily integrated into most conditional GAN objectives. Additionally, explicit regularization on generator allows our method to control a balance between visual quality and diversity. We demonstrate the effectiveness of our method on three conditional generation tasks: image to image translation, image inpainting, and future video prediction. We show that simple addition of our regularization to existing models leads to surprisingly diverse generations, substantially outperforming the previous approaches for multi modal conditional generation specifically designed in each individual task.
Performance of Cu cathode/Fe3+/peroxymonosulfate process on iohexol degradation.
Venue: Journal of hazardous materials
Year: 2019

Copper was used as a non inert cathode material in a Cathode/Fe3+/peroxymonosulfate(PMS) system, and the performance of this novel Cu cathode/Fe3+/PMS system was tested with a typical iodinated X ray contrast media (iohexol) as target organics. The reaction mechanisms and the iohexol degradation pathways were investigated. The operational conditions of Cu cathode/Fe3+/PMS process on iohexol degradation were optimized to be 1.0 mM Fe3+ dosage, 3.0 mM PMS dosage and 0.50 mA/cm2 of current input. The much lower current applied in the present study than previous reports would help to save energy and be more economical. Compared with typical inert cathode (Pt cathode) the Cu cathode/Fe3+/PMS process has better performance on both iohexol removal and deiodination, due to that Cu cathode participated in Fe2+ regeneration and PMS activation via surface Cudeg Cu+(s) Cu2+ Cudeg redox cycle. Fe2+ could be produced via reactions between Fe3+ and Cu/Cu+(s) as well as cathodic reduction of Fe3+ SO4 was generated from PMS activation by Fe2+ Cu/Cu+(s) and cathodic reduction. OH was also generated in this process but SO4 played a dominant role in iohexol degradation. The intermediate products of iohexol and its transformation pathways were complex due to the varied reaction mechanisms involving both oxidation and reduction in Cu cathode/Fe3+/PMS process.
Simulation for Optimal Design of Hand Held Surgical Robots
Venue: 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Year: 2009

Hand held surgical robots are manipulators with dexterous effectors to be used by surgeons in minimally invasive surgery and especially in laparoscopy. Mechanical manipulators for laparoscopy have appeared on the markets in recent years with various interfaces and dexterities. 2 examples are RealHandTM and Laparo AngleTM. The question of which interface and control mode is the best has not been answered yet. Also, the effector kinematics has not been studied much. We have made a simulator to study the robot's interface, control mode and kinematics to design a hand held surgical robot for laparoscopic surgery. We asked test subjects to use the simulator and try to make sutures in a virtual environment. Users opinion is that a joystick as interface is easier to use, compared to a jointed interface translating hand's orientation to that of the effector. It appears that a 6 DOF effector coupled to the shaft is necessary and dexterous enough to make sutures in different angles.
Generating Catharsis through Dance
Year: 2017

My research was an investigation of what creates catharsis in dance. I wanted to know: how and why does dance move people? What are the qualities in contemporary dance that lead to a cathartic experience for the viewer? This required an analysis of philosophies related to: dance and its purpose, choreographic aesthetic involving emotion as a driving force, and the nature of catharsis in art. With an ensemble of undergraduate dance majors from UC Irvine, I implemented various methods and ideologies I had gathered, in an effort to choreograph work that would move an audience. I chose choreographic themes based on emotions that could be universally relatable, and in order to convey these emotions, I coached, directed, and taught movement to dancers who would perform my choreography. This process culminated in a thirty minute work, entitled, What Remains. I kept a record of my choreographic process, comparing and contrasting my methods and their effectiveness in extracting a certain level of expressiveness from the twelve young adult dancers performing my work. After the work was performed, I reflected on what had transpired on stage, as well as feedback from audience members.
Ultrasonic exfoliation of carbon fiber: electroanalytical perspectives
Venue: Journal of Applied Electrochemistry
Year: 2020

Electrochemical anodisation techniques are regularly used to modify carbon fiber surfaces as a means of improving electrochemical performance. A detailed study of the effects of oxidation 2 V) in alkaline media has been conducted and Raman, XPS and SEM analyses of the modification process have been tallied with the resulting electrochemical properties. The co application of ultrasound during the oxidative process has also been investigated to determine if the cavitational and mass transport features influence both the physical and chemical nature of the resulting fibers. Marked discrepancies between anodisation with and without ultrasound is evident in the C1s spectra with variations in the relative proportions of the electrogenerated carbon oxygen functionalities. Mechanisms that could account for the variation in surface species are considered.