nils-herrmann/clean_scirepeval huggingface dataset:
Style and non-style in anatomical illustration: From Renaissance Humanism to Henry Gray.

Style is a familiar category for the analysis of art. It is less so in the history of anatomical illustration. The great Renaissance and Baroque picture books of anatomy illustrated with stylish woodcuts and engravings, such as those by Charles Estienne, Andreas Vesalius and Govard Bidloo, showed figures in dramatic action in keeping with philosophical and theological ideas about human nature. Parallels can be found in paintings of the period, such as those by Titian, Michelangelo and Hans Baldung Grien. The anatomists also claimed to portray the body in an objective manner, and showed themselves as heroes of the discovery of human knowledge. Rembrandt's painting of Dr Nicholas Tulp is the best-known image of the anatomist as hero. The British empirical tradition in the 18th century saw William Cheselden and William Hunter working with techniques of representation that were intended to guarantee detailed realism. The ambition to portray forms life-size led to massive volumes, such as those by Antonio Mascagni. John Bell, the Scottish anatomist, criticized the size and pretensions of the earlier books and argued for a plain style adapted to the needs of teaching and surgery. Henry Gray's famous Anatomy of 1858, illustrated by Henry Vandyke Carter, aspired to a simple descriptive mode of functional representation that avoided stylishness, resulting in a style of its own. Successive editions of Gray progressively saw the replacement of Gray's method and of all his illustrations. The 150th anniversary edition, edited by Susan Standring, radically re-thinks the role of Gray's book within the teaching of medicine.
Interspace between Popliteal Artery and posterior Capsule of the Knee (IPACK) Injectate Spread: A Cadaver Study.

Local anesthetic injection into the interspace between the popliteal artery and the posterior capsule of the knee (IPACK) has the potential to provide motor-sparing analgesia to the posterior knee after total knee arthroplasty. The primary objective of this cadaveric study was to evaluate injectate spread to relevant anatomic structures with IPACK injection.



After receipt of Institutional Review Board Biospecimen Subcommittee approval, IPACK injection was performed on fresh-frozen cadavers. The popliteal fossa in each specimen was dissected and examined for injectate spread.



Ten fresh-frozen cadaver knees were included in the study. Injectate was observed to spread in the popliteal fossa at a mean ± SD of 6.1 ± 0.7 cm in the medial-lateral dimension and 10.1 ± 3.2 cm in the proximal-distal dimension. No injectate was noted to be in contact with the proximal segment of the sciatic nerve, but 3 specimens showed injectate spread to the tibial nerve. In 3 specimens, the injectate showed possible contact with the common peroneal nerve. The middle genicular artery was consistently surrounded by injectate.



This cadaver study of IPACK injection demonstrated spread throughout the popliteal fossa without proximal sciatic involvement. However, the potential for injectate to spread to the tibial or common peroneal nerve was demonstrated. Consistent surrounding of the middle genicular artery with injectate suggests a potential mechanism of analgesia for the IPACK block, due to the predictable relationship between articular sensory nerves and this artery. Further study is needed to determine the ideal site of IPACK injection.
A fifth-order air-filled SIW filter for future 5G applications

This paper presents a fifth-order Tchebyshev bandpass filter based on air-filled substrate integrated waveguide (AFSIW) technology. The iris inductive coupling topology is chosen for filter implementation. The design concept is also introduced based on K-inverted model and Marcuvitz design flow. A comparison between the conventional dielectric-filled substrate integrated waveguide (DFSIW) and the improved AFSIW technology is presented in order to highlight the superiority in term of performance from AFSIW transmission lines. The filter has a relative bandwidth (BW) of 2.98% at 27.92 GHz. The insertion losses is smaller than −1.15 dB in the passband. This bandpass filter can be used for future 5G network or space applications.
Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and α-aminoadipic acid—precursors for penicillin biosynthesis—as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling β-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
Feminizing Genital Gender-Confirmation Surgery.

For many patients with gender dysphoria, gender-confirmation surgery (GCS) helps align their physical characteristics with their gender identity and is a fundamental element of comprehensive treatment. This article is the 2nd in a 3-part series about the treatment of gender dysphoria. Non-operative management was covered in part 1. This section begins broadly by reviewing surgical eligibility criteria, benefits of GCS, and factors associated with regret for transgender men and women. Then, the scope narrows to focus on aspects of feminizing genital GCS, including a discussion of vaginoplasty techniques, complications, and sexual function outcomes. Part 3 features operative considerations for masculinizing genital GCS.



To summarize the World Professional Association for Transgender Health's (WPATH) surgical eligibility criteria and describe how patients with gender dysphoria benefit from GCS, provide an overview of genital and non-genital feminizing gender-confirmation procedures, and review vaginoplasty techniques, preoperative considerations, complications, and outcomes.



A review of relevant literature through April 2017 was performed using PubMed.



Review of literature related to surgical eligibility criteria for GCS, benefits of GCS, and surgical considerations for feminizing genitoplasty.



Most transgender men and women who satisfy WPATH eligibility criteria experience improved quality of life, overall happiness, and sexual function after GCS; regret is rare. Penile inversion vaginoplasty is the preferred technique for feminizing genital GCS according to most surgeons, including the authors whose surgical technique is described. Intestinal vaginoplasty is reserved for certain scenarios. After vaginoplasty most patients report overall high satisfaction with their sexual function even when complications occur, because most are minor and easily treatable.



GCS alleviates gender dysphoria for appropriately selected transgender men and women. Preoperative, intraoperative, and postoperative considerations of feminizing genital gender-confirmation procedures were reviewed. Hadj-Moussa M, Ohl DA, Kuzon WM. Feminizing Genital Gender-Confirmation Surgery.  Rev 2018;6:457-468.
A Focused Planar Microstrip Array for 2.4 GHz RFID Readers

The specific problems encountered in the design of near-field focused planar microstrip arrays for RFID (Radio Frequency IDentification) readers are described. In particular, the paper analyzes the case of a prototype operating at 2.4 GHz, which has been designed and characterized. Improvements with respect to conventional far-field focused arrays (equal phase arrays) are discussed and quantified.
An efficient representation for irradiance environment maps

We consider the rendering of diffuse objects under distant illumination, as specified by an environment map. Using an analytic expression for the irradiance in terms of spherical harmonic coefficients of the lighting, we show that one needs to compute and use only 9 coefficients, corresponding to the lowest-frequency modes of the illumination, in order to achieve average errors of only 1%. In other words, the irradiance is insensitive to high frequencies in the lighting, and is well approximated using only 9 parameters. In fact, we show that the irradiance can be procedurally represented simply as a quadratic polynomial in the cartesian components of the surface normal, and give explicit formulae. These observations lead to a simple and efficient procedural rendering algorithm amenable to hardware implementation, a prefiltering method up to three orders of magnitude faster than previous techniques, and new representations for lighting design and image-based rendering.
Cytomegalovirus Load in Inflamed Intestinal Tissue Is Predictive of Resistance to Immunosuppressive Therapy in Ulcerative Colitis

Previous studies have suggested an association between cytomegalovirus (CMV) infection and steroid-refractory inflammatory bowel disease. In this study, the use of CMV DNA load during acute flare-ups of ulcerative colitis (UC) to predict resistance to immunosuppressive therapy was evaluated in intestinal tissue.Forty-two consecutive patients (sex ratio M/F: 0.9, mean age: 43.6 years) hospitalized for moderate to severe UC and treated with IV steroids were included prospectively. A colonoscopy was performed for each patient at inclusion; colonic biopsy samples of the pathological tissue, and if possible, of the healthy mucosa, were tested for histological analysis and determination of CMV DNA load by real-time polymerase chain reaction assay. Patients were treated as recommended by the current guidelines.Sixteen patients were found positive for CMV DNA in inflamed intestinal tissue but negative in endoscopically healthy tissue; all of these patients were positive for anti-CMV IgG, three exhibited CMV DNA in blood, and none was positive for intestinal CMV antigen by immunohistochemistry detection. In the 26 remaining patients, no stigmata of recent CMV infection were recorded by any technique. By multivariate analysis, the only factor associated with CMV DNA in inflammatory tissue was the resistance to steroids or to three lines of treatment (risk ratio: 4.7; 95% confidence interval: 1.2–22.5). A CMV DNA load above 250 copies/mg in tissue was predictive of resistance to three successive regimens (likelihood ratio+=4.33; area under the receiver-operating characteristic curve=0.85). Eight UC patients with CMV DNA in inflamed tissue and therapeutic failure received ganciclovir; a clinical remission was observed in seven cases, with a sustained response in five of them.The CMV DNA load determined in inflamed intestinal tissue predicts resistance to steroid treatment and to three drug regimens in UC. Initiation of an early antiviral treatment in these patients might delay the occurrence of resistance to current treatments.
Entropy-guided Retinex anisotropic diffusion algorithm based on partial differential equations (PDE) for illumination correction

This report describes the experimental results obtained using a proposed variational Retinex algorithm for controlled illumination correction. Two colour restoration and enhancement schemes of the algorithm are presented for drastically improved results. The algorithm modifies the reflectance image using global and local contrast enhancement approaches and gradually removes the residual illumination to yield highly pleasing results. The proposed algorithms are optimized by way of simultaneous perceptual quality metric (PQM) stabilization and entropy maximization for fully automated processing solving the problem of determination of stopping time. The usage of the HSI or HSV colour space ensures a unique solution to the optimization problem unlike in the RGB space where there is none (forcing manual selection of number of iteration. The proposed approach preserves and enhances details in both bright and dark regions of underexposed images in addition to eliminating the colour distortion, over-exposure in bright image regions, halo effect and grey-world violations observed in Retinex-based approaches. Extensive experiments indicate consistent performance as the proposed approach exploits and augments the advantages of PDEbased formulation, performing illumination correction, colour enhancement correction and restoration, contrast enhancement and noise suppression. Comparisons shows that the proposed approach surpasses most of the other conventional algorithms found in the literature.
A temperature compensated relaxation oscillator for SoC implementations

A temperature and supply independent on-chip reference relaxation oscillator for low voltage design is described. The frequency of oscillation is mainly a function of a PVT robust biasing current. The comparator for the relaxation oscillator is replaced with a high speed common-source stage to eliminate the temperature dependency of the comparator delay. The current sources and voltages are biased by a PVT robust references derived from a bandgap circuitry. This oscillator is designed in TSMC 65 nm CMOS process to operate with a minimum supply voltage of 1.4 V and consumes 100 μW at 157 MHz frequency of oscillation. The oscillator exhibits frequency variation of 1.6% for supply changes from 1.4 V to 1.9 V, and ±1.2% for temperature changes from 20°C to 120°C.
3D-PRNN: Generating Shape Primitives with Recurrent Neural Networks

The success of various applications including robotics, digital content creation, and visualization demand a structured and abstract representation of the 3D world from limited sensor data. Inspired by the nature of human perception of 3D shapes as a collection of simple parts, we explore such an abstract shape representation based on primitives. Given a single depth image of an object, we present 3DPRNN, a generative recurrent neural network that synthesizes multiple plausible shapes composed of a set of primitives. Our generative model encodes symmetry characteristics of common man-made objects, preserves long-range structural coherence, and describes objects of varying complexity with a compact representation. We also propose a method based on Gaussian Fields to generate a large scale dataset of primitive-based shape representations to train our network. We evaluate our approach on a wide range of examples and show that it outperforms nearest-neighbor based shape retrieval methods and is on-par with voxelbased generative models while using a significantly reduced parameter space.
Herd Behavior and Investment : Reply By

In our 1990 paper, we showed that managers concerned with their reputations might choose to mimic the behavior of other managers and ignore their own information. We presented a model in which “smart” managers receive correlated, informative signals, whereas “dumb” managers receive independent, uninformative signals. Managers have an incentive to follow the herd to indicate to the labor market that they have received the same signal as others, and hence are likely to be smart. This model of reputational herding has subsequently found empirical support in a number of recent papers, including Judith A. Chevalier and Glenn D. Ellison’s (1999) study of mutual fund managers and Harrison G. Hong et al.’s (2000) study of equity analysts. We argued in our 1990 paper that reputational herding “requires smart managers’ prediction errors to be at least partially correlated with each other” (page 468). In their Comment, Marco Ottaviani and Peter Sørensen (hereafter, OS) take issue with this claim. They write: “correlation is not necessary for herding, other than in degenerate cases.” It turns out that the apparent disagreement hinges on how strict a definition of herding one adopts. In particular, we had defined a herding equilibrium as one in which agentB alwaysignores his own information and follows agent A. (See, e.g., our Propositions 1 and 2.) In contrast, OS say that there is herding when agent B sometimesignores his own information and follows agent A. The OS conclusion is clearly correct given their weaker definition of herding. At the same time, however, it also seems that for the stricter definition that we adopted in our original paper, correlated errors on the part of smart managers are indeed necessary for a herding outcome—even when one considers the expanded parameter space that OS do. We will try to give some intuition for why the different definitions of herding lead to different conclusions about the necessity of correlated prediction errors. Along the way, we hope to convince the reader that our stricter definition is more appropriate for isolating the economic effects at work in the reputational herding model. An example is helpful in illustrating what is going on. Consider a simple case where the parameter values are as follows: p 5 3⁄4; q 5 1⁄4; z 5 1⁄2, andu 5 1⁄2. In our 1990 paper, we also imposed the constraint that z 5 ap 1 (1 2 a)q, which further implies thata 5 1⁄2. The heart of the OS Comment is the idea that this constraint should be disposed of—i.e., we should look at other values of a. Without loss of generality, we will consider values of a above 1⁄2, and distinguish two cases.
The in vitro propagation of amaryllis (Hippeastrum spp. Hybrids)

A new, rapid technique for the propagation of amaryllis (Hippeastrum spp. hybrids) by means of tissue culture is reported. Leaf bases, scapes, peduncles, inner bulb scales and ovaries were cultured successfully in vitro and plantlets were induced readily at various concentrations of growth regulators. Some plantlets also were produced in the absence of growth regulators. The most productive tissues for propagation were inverted scapes and peduncles, cultured in a modified Murashige and Skoog salt solution with added organic constituents and 1 mg per 1 (4.5μM) 2,4-dichlorophenoxyacetic acid (2,4-D) and 1 mg per 1 (4.4μM) 6-benzylaminopurine (BAP). Plantlets induced axenically also grew roots on the generalized shoot-inducing medium so that no special rooting medium was required. Although friable callus was obtained from ovary tissue cultured on a medium containing 2 mg per 1 (11μM) naphthaleneacetic acid and 4 mg per 1 (18μM) BAP, it produced shoots after 8 weeks of further subculture on the same medium. An average of 10 rooted plantlets was obtained from each scape or peduncle explant on the shoot-propagating medium. Thus, if 45 explants are obtained from each bulb, 450 rudimentary plantlets could be obtained from each mother bulb in 8 weeks of culture. This is a substantial increase over present propagation methods.
Identification and localization of bioactive naphthoquinones in the roots and rhizosphere of Paterson’s curse (Echium plantagineum), a noxious invader

Bioactive plant secondary products are frequently the drivers of complex rhizosphere interactions, including those with other plants, herbivores and microbiota. These chemically diverse molecules typically accumulate in a highly regulated manner in specialized plant tissues and organelles. We studied the production and localization of bioactive naphthoquinones (NQs) in the roots of Echium plantagineum, an invasive endemic weed in Australia. Roots of E. plantagineum produced red-coloured NQs in the periderm of primary and secondary roots, while seedling root hairs exuded NQs in copious quantities. Confocal imaging and microspectrofluorimetry confirmed that bioactive NQs were deposited in the outer layer of periderm cells in mature roots, resulting in red colouration. Intracellular examination revealed that periderm cells contained numerous small red vesicles for storage and intracellular transport of shikonins, followed by subsequent extracellular deposition. Periderm and root hair extracts of field- and phytotron-grown plants were analysed by UHPLC/Q-ToF MS (ultra high pressure liquid chromatography coupled to quadrupole time of flight mass spectrometry) and contained more than nine individual NQs, with dimethylacrylshikonin, and phytotoxic shikonin, deoxyshikonin and acetylshikonin predominating. In seedlings, shikonins were first found 48h following germination in the root-hypocotyl junction, as well as in root hair exudates. In contrast, the root cortices of both seedling and mature root tissues were devoid of NQs. SPRE (solid phase root zone extraction) microprobes strategically placed in soil surrounding living E. plantagineum plants successfully extracted significant levels of bioactive shikonins from living roots, rhizosphere and bulk soil surrounding roots. These findings suggest important roles for accumulation of shikonins in the root periderm and subsequent rhizodeposition in plant defence, interference, and invasion success.
PIECE 2.0: an update for the plant gene structure comparison and evolution database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
The Importance of Being Modest

/ n this chapter, we consider modesty and its importance. We begin by defining modesty, proceed to argue that being modest is hard work, and then lay out some reasons why this is so. Next, we make the case that modesty correlates with, and may even cause, several desirable outcomes—intrapersonal, interpersonal, and group. We conclude by attempting to reconcile the discrepancies between two empirical literatures, one suggesting that modesty entails social and mental health benefits, the other suggesting that self-enhancement does.