bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1α CAD
Authors: Lindström Ida , Andersson Eva , Dogan Jakob 
Published: May 2018

AbstractIntrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1α (Hif-1α CAD). A total of 17 Hif-1α CAD point-mutations were generated and a Φ-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1α CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is “disordered-like”, with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.
Critical role of climate change in plant selection and millet domestication in North China
Authors: Yang Xiaoyan , Wu Wenxiang , Perry Linda , Ma Zhikun , Bar-Yosef Ofer , Cohen David J. , Zheng Hongbo , Ge Quansheng 
Published: May 2018

AbstractWhile North China is one of the earliest independent centers for cereal domestication in the world, the earliest stages of the long process of agricultural origins remain unclear. While only millets were eventually domesticated in early sedentary societies there, recent archaeobotanical evidence reported here indicates that grasses from the Paniceae (including millets) and Triticeae tribes were exploited together by foraging groups from the Last Glacial Maximum to the mid-Holocene. Here we explore how and why millets were selected for domestication while Triticeae were abandoned. We document the different exploitation and cultivation trajectories of the two tribes employing ancient starch data derived from nine archaeological sites dating from 25,000 to 5500 cal BP (LGM through mid-Holocene) in North China. With this diachronic overview, we can place the trajectories into the context of paleoclimatic reconstructions for this period. Entering the Holocene, climatic changes increased the yield stability, abundance, and availability of the wild progenitors of millets, with growing conditions increasingly favoring millets while becoming more unfavorable for grasses of the Triticeae tribe. We thus hypothesize that climate change played a critical role in the selection of millet species for domestication in North China, with early domestication evidenced by 8700 cal BP.
Anti-reflectance investigation of a micro-nano hybrid structure fabricated by dry/wet etching methods
Authors: Tan Xiao , Tao Zhi , Yu Mingxing , Wu Hanxiao , Li Haiwang 
Published: May 2018

AbstractBlack silicon fabrication and manipulation have been well reported by institutes around the world and are quite useful for solar absorption and photovoltaic conversion. In this study, silicon micro-nano hybrid structures were fabricated, and the morphologies of the hybrid structures were analyzed. This paper studied nanostructures formed on tips, pits and a flat surface using a dry etching method and a wet etching method. In terms of nanostructure morphology, nanostructures etched by the wet etching method (13 μm) were taller than those etched by the dry etching method (1 μm), but the wet etched morphology was less organized. After the nanostructures were grown, six samples with nano sturctures and three samples with micro sturctures were measured by a photometer for reflectivity testing. The nine samples were compared and analyzed using the integral of reflectivity and solar emissivity at the earth’s surface. The results show that the nanostructures grown on a tip surface using the wet etching method had the minimum reflectivity in the wavelength range of 300 nm–1100 nm, in consideration of the forbidden energy gap of silicon.
High Quality 3D Photonics using Nano Imprint Lithography of Fast Sol-gel Materials
Authors: Bar-On Ofer , Brenner Philipp , Siegle Tobias , Gvishi Raz , Kalt Heinz , Lemmer Uli , Scheuer Jacob 
Published: May 2018

AbstractA method for the realization of low-loss integrated optical components is proposed and demonstrated. This approach is simple, fast, inexpensive, scalable for mass production, and compatible with both 2D and 3D geometries. The process is based on a novel dual-step soft nano imprint lithography process for producing devices with smooth surfaces, combined with fast sol-gel technology providing highly transparent materials. As a concrete example, this approach is demonstrated on a micro ring resonator made by direct laser writing (DLW) to achieve a quality factor improvement from one hundred thousand to more than 3 million. To the best of our knowledge this also sets a Q-factor record for UV-curable integrated micro-ring resonators. The process supports the integration of many types of materials such as light-emitting, electro-optic, piezo-electric, and can be readily applied to a wide variety of devices such as waveguides, lenses, diffractive elements and more.
Quantum-Optically Enhanced STORM (QUEST) for Multi-Emitter Localization
Authors: Aßmann Marc 
Published: May 2018

AbstractSuper-resolution imaging has introduced new capabilities to investigate processes at the nanometer scale by optical means. However, most super-resolution techniques require either sparse excitation of few emitters or analysis of high-order cumulants in order to identify several emitters in close vicinity. Here, we present an approach that draws upon methods from quantum optics to perform localization super-resolution imaging of densely packed emitters and determine their number automatically: Quantum-optically enhanced STORM (QUEST). By exploiting normalized photon correlations, we predict a localization precision below 30 nm or better even for closely spaced emitter up to a density of 125 emitters per μm at photon emission rates of 105 photons per second and emitter. Our technique does not require complex experimental arrangements and relies solely on spatially resolved time streams of photons and subsequent data analysis.
Testicular sperm is superior to ejaculated sperm for ICSI in cryptozoospermia: An update systematic review and meta-analysis
Authors: Kang Yi-No , Hsiao Ya-Wen , Chen Chien-Yu , Wu Chien-Chih 
Published: May 2018

AbstractIntracytoplasmic sperm injection (ICSI) is well established and provides patients with severely impaired sperm quality with an opportunity to father a child. However, previous studies do not clearly indicate whether male with cryptozoospermia should use testicular sperm or ejaculated sperm for ICSI. The newest systematic review of this topic also gave a controversial conclusion that was based on incorrect pooling result. Moreover, two clinical studies published after the systematic review. In the present update systematic review and meta-analysis, a comprehensive citation search for relevant studies was performed using the Cochrane library databases, Embase, Ovid MEDLINE, PubMed, ScienceDirect, Scopus, and Web of Science up to September 2017. The search returned 313 records, in which six studies were included in quantitative synthesis. These studies involved 578 male infertility patients who had undergone 761 ICSI cycles. The risk ratios favour fresh testicular sperm for good quality embryo rate (1.17, 95% CI 1.05–1.30, P = 0.005), implantation rate (95% CI 1.02–2.26, P = 0.04), and pregnancy rate (RR = 1.74, 95% CI 1.20–2.52, P = 0.004). In conclusion, the existing evidence suggests that testicular sperm is better than ejaculated sperm for ICSI in male with cryptozoospermia.
Eradication of hepatitis C virus is associated with the attenuation of steatosis as evaluated using a controlled attenuation parameter
Authors: Shimizu Kohei , Soroida Yoko , Sato Masaya , Hikita Hiromi , Kobayashi Tamaki , Endo Momoe , Sato Mamiko , Gotoh Hiroaki , Iwai Tomomi , Tateishi Ryosuke , Koike Kazuhiko , Yatomi Yutaka , Ikeda Hitoshi 
Published: May 2018

AbstractChronic hepatitis C virus (HCV) infection was shown to cause hepatic steatosis or suppression of serum lipid levels. However, little is known about the changes in hepatic steatosis following HCV eradication. We aimed to evaluate this issue using the controlled attenuation parameter (CAP), which was recently shown to provide a standardized non-invasive measure of hepatic steatosis. We enrolled 70 patients with chronic HCV infections and steatosis (CAP of over 248 dB/m) who had achieved a sustained viral response at 12 weeks after discontinuation of antiviral treatment using direct-acting antivirals (DAA). We then evaluated the state of hepatic steatosis before and after HCV eradication. We also investigated the changes in serum parameters such as cholesterol and glucose levels. The median value of CAP level decreased significantly after HCV eradication from 273 dB/m to 265 dB/m (P = 0.034). Also, LDL and HDL cholesterol levels increased significantly after HCV eradication (P = 0.002 and P = 0.027, respectively). In conclusion, a decrease in hepatic steatosis after HCV eradication with DAA was revealed in chronic hepatitis C patients with significant steatosis. Cancellation of the viral effect is a possible underlying cause of hepatic steatosis improvement and increase in HDL and LDL cholesterol levels.
Relation Between Iliopsoas Cross-sectional Area and Kicked Ball Speed in Soccer Players
Authors: Wakahara Taku , Chiba Manabu 
Published: May 2018

AbstractThis study aimed to investigate the relationship between the maximal anatomical cross-sectional area (ACSA) of the iliopsoas muscle and ball speed in side-foot and instep kicks. The ACSA of the psoas major and iliacus was measured in 29 male collegiate soccer players by using magnetic resonance imaging. They performed maximal side-foot and instep kicks to a stationary ball. The kicked ball speed was measured with a high-speed camera. Ball speed in the side-foot and instep kicks was significantly correlated with body height (side-foot kick: r=0.650, P<0.001; instep kick: r=0.583, P<0.001). After adjustment for body height, the maximal ACSA of the psoas major was significantly correlated with ball speed in the side-foot kick (r=0.441, P=0.017), but not in the instep kick. The maximal ACSA of the iliacus was not correlated with ball speed in side-foot or instep kicks, even after adjustment for body height. Our results suggest that: 1) body height is a significant determinant of the ball speed in side-foot and instep kicks, and 2) for a given body height, the maximal ACSA of the dominant psoas major is a factor that affects the ball speed in side-foot kick.
Deciphering the Redox Chain Mechanism in the Catalytic Alkylation of Quinones
Authors: Li Zhi , Xu Xiao-Long 
Published: May 2018

Alkylation of p-quinones with allylic and benzylic esters is achieved by using a strong Lewis acid as the catalyst. This transformation likely follows an unusual redox chain mechanism. In this mechanism, quinone undergoes a sequence of reactions: it is reduced to ­hydroquinone (HQ), functionalized in a Lewis acid-catalyzed Friedel–Crafts alkylation, and then oxidized back to quinone. The last step is concurrent with the first step of a second quinone molecule, which is reduced to new HQ and functionalized, and thus propagates the redox chain reaction. The autoinitiation mechanism of the redox chain is not well understood, but additive HQ or Hantzsch ester can serve as effective initiators. The likelihood of this mechanism was elaborated by ­kinetic studies and various control experiments.1	Introduction2	Discovery of Catalytic Alkylation Reactions of Quinones3	Proposed Redox Chain Reaction Mechanism and Experimental Evidence4	Substrate Scope5	Conclusion
Simplifying Lip Reconstruction: An Algorithmic Approach
Authors: Sanniec Kyle , Carboy Jourdan , Thornton James 
Published: May 2018

AbstractThe authors provide an overview of lip reconstruction after Mohs surgery based on the senior author's practice. Lip reconstruction offers unique challenges to preserve not only lip function but also aesthetics. Lip reconstruction must take into consideration the three anatomical layers that comprise the lip and defects that involve the mucosa, the muscle, the skin or more than one layer will help determine the modality of repair. The authors offer an algorithm based on defect location, tissue involvement, and severity of defect to simplify an often complex decision-making process.
Comparison of Outcomes of Total Hip Arthroplasty to Hemiarthroplasty for Geriatric Hip Fractures: A Literature Review of Large Database Studies
Authors: Haynes Monique , Grauer Jonathan 
Published: May 2018

AbstractThe objective of this article is to review large database comparisons of total hip arthroplasty (THA) to hemiarthroplasty (HA) for geriatric hip fracture patients. This article followed a systematic review of the literature using published studies identified via PubMed as the data source. A literature search was done iteratively with a systematic use of variations of key search terms. The initial search identified 490 references. Of the 490, 15 full-text papers were reviewed. Ultimately, nine papers were included in the review. Five of the included studies utilized the National Surgical Quality Improvement Program database, one utilized Hospital Episode Statistics, one utilized The National Hospital Discharge Survey, one utilized Swedish Nation Hip Fracture/Arthroplasty Register, and the last utilized the ENCLAVE system of the Centers for Medicare & Medicaid Services. These all included data ranging from 2005 to 2013 and included at least 1,000 patients. Clinical postoperative outcomes of THA and HA were grouped and compared among the nine studies. The studies used multivariable analysis to make comparisons, and it is of note that HA is much more common than THA in this patient population. Primary outcome variables evaluated included major/minor complications, mortality, length of stay, postoperative transfusion, readmission, dislocation, and revision. Overall, major and minor adverse events (or a combination of the two) were lower for THA than for HA patients, and postoperative transfusions were more common for THA patients. Mortality was significantly less for THA patients by 3% to 4%. Length of stay was lower for THA patients. Dislocation rates were higher for THA patients at 30 days, 18 months, 24 months, and 4 years by odds ratios of three to five times. One study found THA patients more likely to undergo reoperation. In select geriatric patients with femoral neck fractures, THA and HA may be appropriately considered. For those patients, studies suggest that THA may be associated with fewer postoperative challenges than HA; however, postoperative transfusion and dislocation rates were noted to be higher for THA patients.
Long-Term Outcomes of Patients with Squamous Cell Carcinoma of the Temporal Bone after Concomitant Chemoradiotherapy
Authors: Katagiri Katsunori , Saitoh Daisuke , Ogawa Takenori , Higashi Kenjiro , Ariga Hisanori , Shiga Kiyoto 
Published: May 2018

Objectives This article aims to clarify the long-term outcomes of patients with squamous cell carcinoma of the temporal bone who underwent concomitant chemoradiotherapy (CCRT).
Design and Setting The study design was a retrospective chart review.
Patients and Methods From December 2001 to June 2014, 23 patients with cancer of the temporal bone who were treated by CCRT at the Tohoku University Hospital and the Iwate Medical University Hospital were enrolled in this study. For advanced cancer of the temporal bone, a modified docetaxel, cisplatin, and 5-fluorouracil (TPF) regimen was used for CCRT. The long-term outcomes, including prognoses and late complications, were analyzed after CCRT of patients with cancers of the temporal bone.
Results The main long-term complications were stenosis of the external auditory canal and conductive hearing loss. No harmful late complications were observed in these patients. Disease-specific survival rates were 84.9% for all patients, 100% for patients of stage I, II, and III (n = 10), and 75.5% for patients of stage IV (n = 13) at 5 years.
Conclusions Our study showed that CCRT is an effective treatment choice for squamous cell carcinoma of the temporal bone. Furthermore, CCRT using the TPF regimen is a safe and effective initial treatment for patients with advanced cancers of the temporal bone.
Uncertainty in forecasts of long-run economic growth
Authors: Christensen P. , Gillingham K. , Nordhaus W. 
Published: May 2018

Significance
This study develops estimates of uncertainty in projections of global and regional per-capita economic growth rates through 2100, comparing estimates from expert forecasts and an econometric approach designed to analyze long-run trends and variability. Estimates from both methods indicate substantially higher uncertainty than is assumed in current studies of climate change impacts, damages, and adaptation. Results from this study suggest a greater than 35% probability that emissions concentrations will exceed those assumed in the most severe of the available climate change scenarios (RCP 8.5), illustrating particular importance for understanding extreme outcomes.
Amazonia is the primary source of Neotropical biodiversity
Authors: Antonelli Alexandre , Zizka Alexander , Carvalho Fernanda Antunes , Scharn Ruud , Bacon Christine D. , Silvestro Daniele , Condamine Fabien L. 
Published: May 2018

Significance
Amazonia is not only the world’s most diverse rainforest but is also the region in tropical America that has contributed most to its total biodiversity. We show this by estimating and comparing the evolutionary history of a large number of animal and plant species. We find that there has been extensive interchange of evolutionary lineages among different regions and biomes, over the course of tens of millions of years. Amazonia stands out as the primary source of diversity, which can be mainly explained by the total amount of time Amazonian lineages have occupied the region. The exceedingly rich and heterogeneous diversity of the American tropics could only be achieved by high rates of dispersal events across the continent.
Socioeconomic status moderates age-related differences in the brain’s functional network organization and anatomy across the adult lifespan
Authors: Chan Micaela Y. , Na Jinkyung , Agres Phillip F. , Savalia Neil K. , Park Denise C. , Wig Gagan S. 
Published: May 2018

Significance
An individual’s socioeconomic status (SES) is a central feature of their environmental surroundings and has been shown to relate to the development and maturation of their brain in childhood. Here, we demonstrate that an individual’s present (adult) SES relates to their brain function and anatomy across a broad range of middle-age adulthood. In middle-aged adults (35–64 years), lower SES individuals exhibit less organized functional brain networks and reduced cortical thickness compared with higher SES individuals. These relationships cannot be fully explained by differences in health, demographics, or cognition. Additionally, childhood SES does not explain the relation between SES and brain network organization. These observations provide support for a powerful relationship between the environment and the brain that is evident in adult middle age.
Pacing of Paleozoic macroevolutionary rates by Milankovitch grand cycles
Authors: Crampton James S. , Meyers Stephen R. , Cooper Roger A. , Sadler Peter M. , Foote Michael , Harte David 
Published: May 2018

SignificanceThere has been long-standing debate about the relative roles of intrinsic biotic interactions vs. extrinsic environmental factors as drivers of biodiversity change. Here, we show that, relatively early in the history of complex life, Milankovitch “grand cycles” associated with astronomical rhythms explain between 9 and 16% of variation in species turnover probability (extinction probability plus speciation probability) in a major Early Paleozoic zooplankton group, the graptoloids. These grand cycles would have modulated climate variability, alternating times of relative stability in the environment with times of maximum volatility, which influenced oceanic circulation and structure and thus, phytoplankton populations at the base of the marine food web.
Spatial mutation patterns as markers of early colorectal tumor cell mobility
Authors: Ryser Marc D. , Min Byung-Hoon , Siegmund Kimberly D. , Shibata Darryl 
Published: May 2018

Significance
Thanks to improved screening technologies, many small “premalignant” tumors are now detected and treated, which reduces late-stage disease and cancer mortality, but also leads to overdiagnosis. Indeed, it remains uncertain if the starts of benign and malignant tumors differ. Here, we combine mathematical multiscale models with multiregional sequencing to infer that the starts of benign and some malignant tumors differ. The abnormal cell mobility eventually needed for invasion and metastasis is already expressed at the start of growth for some malignant tumors but not benign tumors. Therefore, some malignant tumors start with more invasive potential (“born to be bad”), and this early abnormal cell mobility can potentially be used to identify patients more likely to benefit from aggressive treatment.
Weak Galilean invariance as a selection principle for coarse-grained diffusive models
Authors: Cairoli Andrea , Klages Rainer , Baule Adrian 
Published: May 2018

Significance
Galilean invariance is a cornerstone of classical mechanics. It states that for closed systems the equations of motion of the microscopic degrees of freedom do not change under Galilean transformations to different inertial frames. However, the description of real world systems usually requires coarse-grained models integrating complex microscopic interactions indistinguishably as friction and stochastic forces, which intrinsically violate Galilean invariance. By studying the coarse-graining procedure in different frames, we show that alternative rules—denoted as “weak Galilean invariance”—need to be satisfied by these stochastic models. Our results highlight that diffusive models in general cannot be chosen arbitrarily based on the agreement with data alone but have to satisfy weak Galilean invariance for physical consistency.
Pseudomonas aeruginosa
transcriptome during human infection
Authors: Cornforth Daniel M. , Dees Justine L. , Ibberson Carolyn B. , Huse Holly K. , Mathiesen Inger H. , Kirketerp-Møller Klaus , Wolcott Randy D. , Rumbaugh Kendra P. , Bjarnsholt Thomas , Whiteley Marvin 
Published: May 2018

Significance
Microbiologists typically use laboratory systems to study the bacteria that infect humans. Over time, this has created a gap between what researchers understand about bacteria growing in the laboratory and those growing in humans. It is well-known that the behavior of bacteria is shaped by their environment, but how this behavior differs in laboratory models compared with human infections is poorly understood. We compared transcription data from a variety of human infections with data from a range of in vitro samples. We found important differences in expression of genes involved in antibiotic resistance, cell–cell communication, and metabolism. Understanding the bacterial expression patterns in human patients is a necessary step toward improved therapy and the development of more accurate laboratory models.