nils-herrmann/clean_scirepeval huggingface dataset:
A highly parallel 4K real time HEVC fractional motion estimation architecture for FPGA implementation
Venue: 2016 IEEE International Conference on Electronics, Circuits and Systems (ICECS)

HEVC is the newest standard developed by the Joint Collaborative Team on Video Coding (JCT VC) mainly characterized by improving the encoding performance and efficiency in almost 50% of its predecessor, H.264/AVC for the same video quality. HEVC is also characterized for targeting Ultra High Definition (UHD) video streams e.g. 4k and 8k resolutions. These improvements resulted from the enhance of encoding processes complexity, which also brings the necessity of more computational resources for its implementation. One of the hot spots in HEVC Encoding is the Fractional Motion Estimation (FME) process, which significantly improves the video compression efficiency at the expense of 40 60% of encoding time in the ITU T standard coding software. In order to optimize this processing time and make it suitable for Real Time UHD Video applications, this work proposes a highly parallel Half and Quarter Pixel Accurate FME architecture targeting FPGA devices. The architecture was described using VHDL and synthesized for the Altera Cyclone IV, V and Arria II FPGA families. The results established a maximum frequency of 298 MHz being able to process 4K (3840x2160) Video Streaming @38fps.
The Recombinant University: Genetic Engineering and the Emergence of Stanford Biotechnology
Venue: Ambix

continuities and intersections. Although written under the Cambridge influence of Jim Secord's "knowledge in transit" paradigm, perhaps more could have been said about the kind of circulation between writers, publishers, and readers that featured in those science themed fairy tales, and in particular about the specific role of women and children as active audiences for science. A more refined analysis of present scholarship on science and literature would have been valuable. Take for instance Barbara Naumann's guest contribution to a special issue of Science in Context (2005) in which several papers explore different "contact zones" and aspects of self reflection and self representation. A certain comparative approach using other cases from outside Victorian Britain might also have been informative and relevant for a complete analysis of that particular genre. Perhaps Lord Byron was right when he said, as Keene quotes: "Truth is stranger than fiction" (p. 187) The truth here is that the book is a remarkable piece of historical research that might interest several audiences beyond the specialized area of history of science and chemistry. This is another sign of the dynamism of present scholarship on the intersections between science and literature, and also of the vitality of the British Society for Literature and Science and the Cambridge Children's Literature Seminar. Keene helps us to pursue the idea that "reasoned scientific books are not easily distinguished from more imaginative or fantastical writings" (p. 8) Her research confirms that literary devices were indeed used in the past, in particular in Victorian Britain, as a metaphor for scientific understanding.
Hair and beauty choices of African American women during the Civil Rights Movement, 1960 1974

This research examined the Civil Rights Movement, specifically focusing on hair and beauty choices of African American women who were emerging adults (ages 18 25) between the years 1960 1974, which bridges both the classical period of the Civil Rights Movement and that of Black Power politics (Wilson, 2013) The specific time period corresponds with the adoption of African American hairstyles that were more Afrocentric, following the social climate of Black Pride (Walker, 2007) To achieve understanding of African American women's perspectives, seven participants were interviewed using Seidman's (2013) protocol for which a three part, in depth interview series was conducted. The successive interviews concentrated on the themes of: 1) hair history throughout their lives, 2) details of experiences during the Civil Rights Movement years 1960 74, and 3) creating reflections on the meaning of hairstyle choices in the participant's life. This dissertation followed a non traditional format that allowed for the completion of two scholarly articles related to African American women's hair. Article one: Ages and stages: African American women and their lives through their hair, examines participants' presentations of self. Communication of meaning and values associated with dress were negotiated between the participants and others, which resulted in their choices of presentation. Goffman's (1959) discussion of the presentation of self was used to explain how marginalized groups strive to act appropriately or ideally to dominant standards and power groups. Participants described how they chose their hairstyles and dress for varying audiences and settings. Their presentation of self was highly influenced by the intersectional subject positions held by the participants, reflecting larger hegemonic norms in U.S. society.
Witchcraft Wealth and Disability Reinterpretation of a folk belief in contemporary urban Africa

Many groups in sub Saharan Africa have historically linked persons with disabilities with witchcraft as a component of a wider link between accusations of witchcraft and socially marginalized populations. It is commonly assumed that traditional prejudices towards persons with disabilities are receding in light of urbanization, education, mass media and efforts to confront such prejudice and stigma by governments, disability advocates and civil society. Ratification of the UN Convention on the Rights of Persons with Disabilities (CRPD) by many African countries is considered an additional impetus for change. While beliefs differ throughout the region, there is an unsettling trend in many urban areas where traditional beliefs linking disability with witchcraft are being reinterpreted. Fuelled by quest for rapid social and economic advancement, urban 'witch doctors' promote beliefs that individuals and families can prosper if they perform rituals or sacrifice involving abuse, mutilation or killing of children and adults with disabilities. These beliefs are reinforced in popular media and some Pentecostal churches where disability is linked to evil spirits or the devil, while 'cure' of disability is linked to virtue and prosperity. Based on literature review and fieldwork in Tanzania and Uganda we argue here that with rapid urbanization, links between witchcraft and disability in contemporary African popular urban culture is an issue of concern that must be acknowledged and addressed.
Systemic Induction of Photosynthesis via Illumination of the Shoot Apex Is Mediated Sequentially by Phytochrome B, Auxin and Hydrogen Peroxide in Tomato1[OPEN]
Venue: Plant Physiology

Red light perceived in the shoot apex by phyB alters IAA and H2O2 signaling, accelerating photosynthetic induction in systemic leaves by increasing CEF dependent ATP production in tomato. Systemic signaling of upper leaves promotes the induction of photosynthesis in lower leaves, allowing more efficient use of light flecks. However, the nature of the systemic signals has remained elusive. Here, we show that preillumination of the tomato (Solanum lycopersicum) shoot apex alone can accelerate photosynthetic induction in distal leaves and that this process is light quality dependent, where red light promotes and far red light delays photosynthetic induction. Grafting the wild type rootstock with a phytochome B (phyB) mutant scion compromised light induced photosynthetic induction as well as auxin biosynthesis in the shoot apex, auxin signaling, and RESPIRATORY BURST OXIDASE HOMOLOG1 (RBOH1) dependent hydrogen peroxide (H2O2) production in the systemic leaves. Light induced systemic H2O2 production in the leaves of the rootstock also was absent in plants grafted with an auxin resistant diageotropica (dgt) mutant scion. Cyclic electron flow around photosystem I and associated ATP production were increased in the systemic leaves by exposure of the apex to red light. This enhancement was compromised in the systemic leaves of the wild type rootstock with phyB and dgt mutant scions and also in RBOH1 RNA interference leaves with the wild type as scion. Silencing of ORANGE RIPENING, which encodes NAD(P)H dehydrogenase, compromised the systemic induction of photosynthesis. Taken together, these results demonstrate that exposure to red light triggers phyB mediated auxin synthesis in the apex, leading to H2O2 generation in systemic leaves. Enhanced H2O2 levels in turn activate cyclic electron flow and ATP production, leading to a faster induction of photosynthetic CO2 assimilation in the systemic leaves, allowing plants better adaptation to the changing light environment.
Plastid osmotic stress influences cell differentiation at the plant shoot apex
Venue: Development

The balance between proliferation and differentiation in the plant shoot apical meristem is controlled by regulatory loops involving the phytohormone cytokinin and stem cell identity genes. Concurrently, cellular differentiation in the developing shoot is coordinated with the environmental and developmental status of plastids within those cells. Here, we employ an Arabidopsis thaliana mutant exhibiting constitutive plastid osmotic stress to investigate the molecular and genetic pathways connecting plastid osmotic stress with cell differentiation at the shoot apex. msl2 msl3 mutants exhibit dramatically enlarged and deformed plastids in the shoot apical meristem, and develop a mass of callus tissue at the shoot apex. Callus production in this mutant requires the cytokinin receptor AHK2 and is characterized by increased cytokinin levels, downregulation of cytokinin signaling inhibitors ARR7 and ARR15, and induction of the stem cell identity gene WUSCHEL. Furthermore, plastid stress induced apical callus production requires elevated plastidic reactive oxygen species, ABA biosynthesis, the retrograde signaling protein GUN1, and ABI4. These results are consistent with a model wherein the cytokinin/WUS pathway and retrograde signaling control cell differentiation at the shoot apex.  During plastid stress induced apical callus production in Arabidopsis, the cytokinin/WUSCHEL pathway and a plastid to nucleus signaling pathway are implicated in cell differentiation at the shoot apex.
RNASeq Analysis of the Shoot Apex of Flax (Linum usitatissimum) to Identify Phloem Fiber Specification Genes
Venue: Front. Plant Sci.

All of the post embryonic, above ground structures of seed plants are generated from the shoot apical meristem (SAM) which acts as a reservoir of stem cells. Members of the flax genus (Linum spp. have been used historically as models for the study of SAMs (Esau, 1942) Cultivated flax (Linum usitatissimum) is grown in more than 50 countries for its seeds or its stem phloem (bast) fibers (Rubilar et al. 2010) Due to prolonged intrusive growth, and a highly crystalline cellulosic secondary wall, flax phloem fibers are among the longest and strongest cells in plants (Mohanty et al. 2000) In flax, all phloem fibers are derived from primary growth in the shoot apex. Specification of phloem fibers occurs in the apical most 0.5 mm of the stem, since young phloem fibers can be anatomically distinguished starting 0.4 0.5 mm from the shoot apex (Gorshkova et al. 2003) The molecular mechanisms that govern fiber identity are almost entirely unknown (Gorshkova et al. 2012) Also, in contrast to the significant progress obtained in the past decade toward understanding xylem differentiation, information about the phloem fiber differentiation is very scarce (De Rybel et al. 2016) In the past decade, shoot apex transcriptomes have been described in various plants, including maize, pea, soybean, rice, Arabidopsis and chickpea, but none of these produce significant primary phloem fibers (Ohtsu et al. 2007; Wong et al. 2008; Haerizadeh et al. 2009; Jiao et al. 2009; Yadav et al. 2009; Wang et al. 2014) Most molecular and cellular research on flax fiber has thus far focused on later stages of development (Day et al. 2005; Roach and Deyholos, 2007; Fenart et al. 2010) Differential transcript expression data from the region of the shoot apex in which fiber specification occurs would complement other approaches (e.g. mutant screening) aimed at understanding primary phloem fiber differentiation.
Structure and functioning of oil cavities in the shoot apex of Metrodorea nigra A. St. Hil. (Rutaceae)
Venue: Protoplasma

This study investigates the histology and subcellular features of secretory cavities during the development of the shoot apex of Metrodorea nigra A. St. Hil. in order to better understand the functioning of these glands. This Rutaceae species is a very suitable model for studying secretory cavity life span, since the shoot apex exhibits both dormant and growth stages during its annual cycle. Shoot apices were collected during the dormant and growth stages from populations of M. nigra growing under natural conditions. Materials were processed using standard techniques for light and electron microscopy. The secretory cavities originate under the protodermis, and their initiation is restricted to the early developmental stage of shoot organs, which are protected by a hood shaped structure. Secretory cavities have a multi seriate epithelium surrounding a lumen that expands schizolysigenously. Oil production begins before lumen formation. When the shoot apex resumes development after the dormant stage, the glands remain active in oil secretion in the developing shoot apex and fully expanded leaves. The mature epithelial cells are flattened and exhibit very thin walls, large oil bodies, leucoplasts surrounded by endoplasmic reticulum, and mitochondria with unusual morphology. The tangential walls of the epithelial cells facing the lumen undergo continuous peeling. The vacuole extrusion appears to be the primary mode of release oil into the lumen, in an exocytotic way. The continuity of oil secretion is ensured by the replacement of the damaged inner epithelial cells by divisions in the parenchyma layer that surround the oil gland, likely a meristematic sheath.
Heterogeneous team deep q learning in low dimensional multi agent environments
Venue: 2016 IEEE Conference on Computational Intelligence and Games (CIG)

Deep Q Learning is an effective reinforcement learning method, which has recently obtained human level performance for a set of Atari 2600 games. Remarkably, the system was trained on the high dimensional raw visual data. Is Deep Q Learning equally valid for problems involving a low dimensional state space? To answer this question, we evaluate the components of Deep Q Learning (deep architecture, experience replay, target network freezing, and meta state) on a Keepaway soccer problem, where the state is described only by 13 variables. The results indicate that although experience replay indeed improves the agent performance, target network freezing and meta state slow down the learning process. Moreover, the deep architecture does not help for this task since a rather shallow network with just two hidden layers worked the best. By selecting the best settings, and employing heterogeneous team learning, we were able to outperform all previous methods applied to Keepaway soccer using a fraction of the runner up's computational expense. These results extend our understanding of the Deep Q Learning effectiveness for low dimensional reinforcement learning tasks.
Sperm with an abnormal hypo osmotic swelling test normal fertilization, normal embryo development, but implantation failure.
Venue: Clinical and experimental obstetrics gynecology

To review the clinical importance of including the hypo osmotic swelling (HOS) test in routine male fertility testing which in general is not evaluated by most physicians dealing with infertility.  Pregnancy rates were evaluated in patients with low HOS test scores. A low HOS test was specifically defined as having less than 50% of sperm exhibiting the normal physiologic response of tail swelling, when subjected to a hypo osmolar solution. Pregnancy rates of patients with low HOS test were examined after intercourse, intrauterine insemination (IUI) conventional oocyte insemination, and in vitro fertilization (IVF) Patients with a low HOS test were also treated with a protein digestive enzyme chymotrypsin. Patients receiving intervention then underwent IUI, IVF with conventional oocyte insemination, or IVF with intracytoplasmic sperm injection (ICSI) Pregnancy rates of the cohort receiving intervention were then examined for comparison.  The HOS test abnormality leads to normal fertilization but almost invariably negatively effects embryo implantation. Treatment with chymotrypsin, or performing IVF with ICSI, can overcome the toxic protein causing the embryo implantation defect. This toxic protein may be cryolabile and freezing sperm or embryos may prove to be another mode of therapy.  The HOS abnormality may be the most reliable semen abnormality predicting failure to conceive even with IVF unless the defect is negated. Therapy is very effective. Unfortunately this test is rarely evaluated by most infertility specialists but it should be. The frequency increases with age.
Herpes zoster ophthalmicus with retrobulbar neuritis.
Venue: Nepalese journal of ophthalmology a biannual peer reviewed academic journal of the Nepal Ophthalmic Society NEPJOPH

Retrobulbar neuritis in Herpes Zoster Ophthalmicus (HZO) has been reported very rarely.  To report a very rare case of HZO with retrobulbar neuritis with detailed clinical features and treatment responses.  A fifty eight year old male presented with Herpes zoster retrobulbarneuritis in the left eye. It was characterized by decreased visual acuity, mid dilated pupil with sluggish reaction, normal optic disc and central scotoma in Humphrey visual field. Visual acuity improved with systemic Acyclovir and steroids.  This is a rare case of HZO associated with retrobulbar neuritis. Prompt treatment with systemic antiviral and steroid improve the visual outcome.
Volumetric flow imaging reveals the importance of vortex ring formation in squid swimming tail first and arms first
Venue: Journal of Experimental Biology

Squids use a pulsed jet and fin movements to swim both arms first (forward) and tail first (backward) Given the complexity of the squid multi propulsor system, 3D velocimetry techniques are required for the comprehensive study of wake dynamics. Defocusing digital particle tracking velocimetry, a volumetric velocimetry technique, and high speed videography were used to study arms first and tail first swimming of brief squid Lolliguncula brevis over a broad range of speeds [0 10 dorsal mantle lengths (DML) s 1] in a swim tunnel. Although there was considerable complexity in the wakes of these multi propulsor swimmers, 3D vortex rings and their derivatives were prominent reoccurring features during both tail first and arms first swimming, with the greatest jet and fin flow complexity occurring at intermediate speeds (1.5 3.0 DML s 1) The jet generally produced the majority of thrust during rectilinear swimming, increasing in relative importance with speed, and the fins provided no thrust at speeds >4.5 DML s 1. For both swimming orientations, the fins sometimes acted as stabilizers, producing negative thrust (drag) and consistently provided lift at low/intermediate speeds <2.0 DML s 1) to counteract negative buoyancy. Propulsive efficiency (e) increased with speed irrespective of swimming orientation, and e for swimming sequences with clear isolated jet vortex rings was significantly greater (e=78.6+ 7.6% mean+ s.d. than that for swimming sequences with clear elongated regions of concentrated jet vorticity (e=67.9+ 19.2% This study reveals the complexity of 3D vortex wake flows produced by nekton with hydrodynamically distinct propulsors.  Multi propulsor squids produce complex 3D vortex wake flows while swimming arms first and tail first, as revealed by 3D jet/fin force and propulsive efficiency measurements.
Bringing next generation diagnostics to the clinic through synthetic biology
Venue: EMBO molecular medicine

The promise for real precision medicine is contingent on innovative technological solutions to diagnosis and therapy. In the post genomic era, rational and systematic approaches to biological design could provide new ways to dynamically probe, monitor, and interface human pathophysiology. Emerging as a mature field increasingly transitioning to the clinics, synthetic biology integrates engineering principles to build sensors, control circuits, and actuators within the biological substrate according to clinical specifications. A particularly tantalizing goal is to develop novel versatile, programmable and autonomous diagnostic devices intertwined with therapy and personalized for the patient to get closest, finest, and most comprehensive diagnostic information and medical procedures. Here, we discuss how synthetic biology could be preparing the future of medicine, supporting and speeding up the development of diagnostics with novel capabilities to bring direct improvement from the clinical laboratory to the patient, while addressing healthcare evolution and global health concerns.
BrisSynBio: a BBSRC/EPSRC funded Synthetic Biology Research Centre
Venue: Biochemical Society transactions

BrisSynBio is the Bristol based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC) funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework.
Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations
Venue: European Journal of Epidemiology

Misinterpretation and abuse of statistical tests, confidence intervals, and statistical power have been decried for decades, yet remain rampant. A key problem is that there are no interpretations of these concepts that are at once simple, intuitive, correct, and foolproof. Instead, correct use and interpretation of these statistics requires an attention to detail which seems to tax the patience of working scientists. This high cognitive demand has led to an epidemic of shortcut definitions and interpretations that are simply wrong, sometimes disastrously so and yet these misinterpretations dominate much of the scientific literature. In light of this problem, we provide definitions and a discussion of basic statistics that are more general and critical than typically found in traditional introductory expositions. Our goal is to provide a resource for instructors, researchers, and consumers of statistics whose knowledge of statistical theory and technique may be limited but who wish to avoid and spot misinterpretations. We emphasize how violation of often unstated analysis protocols (such as selecting analyses for presentation based on the P values they produce) can lead to small P values even if the declared test hypothesis is correct, and can lead to large P values even if that hypothesis is incorrect. We then provide an explanatory list of 25 misinterpretations of P values, confidence intervals, and power. We conclude with guidelines for improving statistical interpretation and reporting.