bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel mechanism for direct real-time polymerase chain reaction that does not require DNA isolation from prokaryotic cells
Authors: Soejima Takashi , Xiao Jin-zhong , Abe Fumiaki 
Published: June 2016

AbstractTypically, polymerase chain reaction (PCR) is performed after DNA isolation. Real-time PCR (qPCR), also known as direct qPCR in mammalian cells with weak membranes, is a common technique using crude samples subjected to preliminary boiling to elute DNA. However, applying this methodology to prokaryotic cells, which have solid cell walls, in contrast to mammalian cells which immediately burst in water, can result in poor detection. We successfully achieved PCR elongation with the addition of 1.3 cfu ofCronobacter muytjensiito a newly developed direct qPCR master mix without performing any crude DNA extraction (detection limit of 1.6 × 100cfu/ml for the test sample compared with a detection limit of 1.6 × 103cfu/ml primarily for crude (boiling) or classical DNA isolation). We revealed that the chromosomal DNA retained in prokaryotic cells can function as a PCR template, similarly to the mechanism inin situPCR. Elucidating this reaction mechanism may contribute to the development of an innovative master mix for direct qPCR to detect genes in a single bacterium with solid cell walls and might lead to numerous novel findings in prokaryotic genomics research.
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
Authors: Fruchtman Amir , Lambert Neill , Gauger Erik M. 
Published: June 2016

AbstractUnderstanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model.
NdhV subunit regulates the activity of type-1 NAD(P)H dehydrogenase under high light conditions in cyanobacterium Synechocystis sp. PCC 6803
Authors: Chen Xin , He Zhihui , Xu Min , Peng Lianwei , Mi Hualing 
Published: June 2016

AbstractThe cyanobacterial NAD(P)H dehydrogenase (NDH-1) complexes play crucial roles in variety of bioenergetic reactions. However, the regulative mechanism of NDH-1 under stressed conditions is still unclear. In this study, we detected that the NDH-1 activity is partially impaired, but the accumulation of NDH-1 complexes was little affected in the NdhV deleted mutant (ΔndhV) at low light in cyanobacterium Synechocystis sp. PCC 6803. ΔndhV grew normally at low light but slowly at high light under inorganic carbon limitation conditions (low pH or low CO2), meanwhile the activity of CO2 uptake was evidently lowered than wild type even at pH 8.0. The accumulation of NdhV in thylakoids strictly relies on the presence of the hydrophilic subcomplex of NDH-1. Furthermore, NdhV was co-located with hydrophilic subunits of NDH-1 loosely associated with the NDH-1L, NDH-1MS′ and NDH-1M complexes. The level of the NdhV was significantly increased at high light and deletion of NdhV suppressed the up-regulation of NDH-1 activity, causing the lowered the photosynthetic oxygen evolution at pH 6.5 and high light. These data indicate that NdhV is an intrinsic subunit of hydrophilic subcomplex of NDH-1, required for efficient operation of cyclic electron transport around photosystem I and CO2 uptake at high lights.
MYB31/MYB42 Syntelogs Exhibit Divergent Regulation of Phenylpropanoid Genes in Maize, Sorghum and Rice
Authors: Agarwal Tina , Grotewold Erich , Doseff Andrea I. , Gray John 
Published: June 2016

AbstractZmMYB31 and ZmMYB42 are R2R3-MYB transcription factors implicated in the regulation of phenylpropanoid genes in maize. Here, we tested the hypothesis that the regulatory function of MYB31 and MYB42 is conserved in other monocots, specifically in sorghum and rice. We demonstrate that syntelogs of MYB31 and MYB42 do bind to phenylpropanoid genes that function in all stages of the pathway and in different tissues along the developmental gradient of seedling leaves. We found that caffeic acid O-methyltransferase (COMT1) is a common target of MYB31 and MYB42 in the mature leaf tissues of maize, sorghum and rice, as evidenced by Chromatin immunoprecipitation (ChIP) experiments. In contrast, 4-coumarate-CoA ligase (4CL2), ferulate-5-hydroxylase (F5H), and caffeoyl shikimate esterase (CSE), were targeted by MYB31 or MYB42, but in a more species-specific fashion. Our results revealed MYB31 and MYB42 participation in auto- and cross-regulation in all three species. Apart from a limited conservation of regulatory modules, MYB31 and MYB42 syntelogs appear to have undergone subfunctionalization following gene duplication and divergence of maize, sorghum, and rice. Elucidating the different regulatory roles of these syntelogs in the context of positive transcriptional activators may help guide attempts to alter the flux of intermediates towards lignin production in biofuel grasses.
Sub-10 nm Ta Channel Responsible for Superior Performance of a HfO2 Memristor
Authors: Jiang Hao , Han Lili , Lin Peng , Wang Zhongrui , Jang Moon Hyung , Wu Qing , Barnell Mark , Yang J. Joshua , Xin Huolin L. , Xia Qiangfei 
Published: June 2016

AbstractMemristive devices are promising candidates for the next generation non-volatile memory and neuromorphic computing. It has been widely accepted that the motion of oxygen anions leads to the resistance changes for valence-change-memory (VCM) type of materials. Only very recently it was speculated that metal cations could also play an important role, but no direct physical characterizations have been reported yet. Here we report a Ta/HfO2/Pt memristor with fast switching speed, record high endurance (120 billion cycles) and reliable retention. We programmed the device to 24 discrete resistance levels, and also demonstrated over a million (220) epochs of potentiation and depression, suggesting that our devices can be used for both multi-level non-volatile memory and neuromorphic computing applications. More importantly, we directly observed a sub-10 nm Ta-rich and O-deficient conduction channel within the HfO2 layer that is responsible for the switching. This work deepens our understanding of the resistance switching mechanism behind oxide-based memristive devices and paves the way for further device performance optimization for a broad spectrum of applications.
White carbon: Fluorescent carbon nanoparticles with tunable quantum yield in a reproducible green synthesis
Authors: Meiling Till T. , Cywiński Piotr J. , Bald Ilko 
Published: June 2016

AbstractIn this study, a new reliable, economic and environmentally-friendly one-step synthesis is established to obtain carbon nanodots (CNDs) with well-defined and reproducible photoluminescence (PL) properties via the microwave-assisted hydrothermal treatment of starch and Tris-acetate-EDTA (TAE) buffer as carbon sources. Three kinds of CNDs are prepared using different sets of above mentioned starting materials. The as-synthesized CNDs: C-CND (starch only), N-CND 1 (starch in TAE) and N-CND 2 (TAE only) exhibit highly homogenous PL and are ready to use without need for further purification. The CNDs are stable over a long period of time (>1 year) either in solution or as freeze-dried powder. Depending on starting material, CNDs with PL quantum yield (PLQY) ranging from less than 1% up to 28% are obtained. The influence of the precursor concentration, reaction time and type of additives on the optical properties (UV-Vis absorption, PL emission spectrum and PLQY) is carefully investigated, providing insight into the chemical processes that occur during CND formation. Remarkably, upon freeze-drying the initially brown CND-solution turns into a non-fluorescent white/slightly brown powder which recovers PL in aqueous solution and can potentially be applied as fluorescent marker in bio-imaging, as a reduction agent or as a photocatalyst.
Critical role of XBP1 in cancer signalling is regulated by PIN1
Authors: Chae Unbin , Park Sun-Ji , Kim Bokyung , Wei Shou , Min Ju-Sik , Lee Jun-Hyeog , Park Se Hoon , Lee Ann-Hwee , Lu Kun Ping , Lee Dong-Seok , Min Sang-Hyun 
Published: June 2016

XBP1 (X-box-binding protein 1) is activated in cancer and has a pivotal role in tumorigenesis and progression of human cancer. In particular, the XBP1 transcriptional regulatory network is well known to drive cancer development, but little is known about whether the stability of XBP1 is regulated and, if so, what controls the stability of XBP1. In the present study we show that PIN1 prolyl isomerase interacts with the active form of XBP1 (XBP1s) in a phosphorylation-dependent manner and promotes XBP1s-induced cell proliferation and transformation through the regulation of XBP1 stability. By contrast, depletion of Pin1 in cancer cells reduced XBP1s expression, which subsequently inhibits cell proliferation and transformation. Interestingly, XBP1s activates multiple oncogenic pathways including NF-κB (nuclear factor κB), AP1 (activator protein 1) and Myc, and down-regulates PIN1 transcription via a negative-feedback mechanism through p53 induction. Ultimately, reciprocal regulation of Pin1 and XBP1s is associated with the activation of oncogenic pathways, and the relationship of PIN1 and XBP1 may be an attractive target for novel therapy in cancers.
GaN planar Schottky barrier diode with cut‐off frequency of 902 GHz
Authors: Liang Shixiong , Fang Yulong , Xing Dong , Zhang Zhirong , Wang Junlong , Guo Hongyu , Zhang Lisen , Gu Guodong , Feng Zhihong 
Published: June 2016

GaN planar Schottky barrier diode (SBD) with an n−/n+ structure was grown and fabricated on sapphire substrate. An n+ GaN epitaxial layer with doping concentration of 8 × 1018 cm−3 was employed to reduce the parasitic resistance. An air‐bridge structure and 50 μm substrate thinning‐down technique were adopted in order to reduce the parasitic capacitance. A record cut‐off frequency (fc) of 902 GHz was achieved for GaN planar SBD with 2 μm anode diameter.
Transcription factor Bcl11b sustains iNKT1 and iNKT2 cell programs, restricts iNKT17 cell program, and governs iNKT cell survival
Authors: Uddin Mohammad Nizam , Sultana Dil Afroz , Lorentsen Kyle J. , Cho Jonathan J. , Kirst Mariana E. , Brantly Mark L. , Califano Danielle , Sant'Angelo Derek B. , Avram Dorina 
Published: June 2016

SignificanceInvariant natural killer T (iNKT) cells are innate-like T cells that recognize lipid antigens and play important roles in antimicrobial and tumor immunity. Functionally, iNKT cells have been classified in three effector subsets based on expression of specific transcription factors (TFs) and cytokine genes. We previously demonstrated that the TF Bcl11b controls glycolipid processing and presentation by double-positive thymocytes to iNKT precursors and thus their formation. Using a model that allows bypassing those defects, here we provide evidence that the TF Bcl11b is critical for effector iNKT1 and INKT2 subsets and overall survival of iNKT cells. Additionally we provide evidence that Bcl11b sustains cytokine production by iNKT1 and iNKT2 cells and restricts expression of the iNKT17 cell program in all effector subsets.
Evidence for a cysteine-mediated mechanism of excitation energy regulation in a photosynthetic antenna complex
Authors: Orf Gregory S. , Saer Rafael G. , Niedzwiedzki Dariusz M. , Zhang Hao , McIntosh Chelsea L. , Schultz Jason W. , Mirica Liviu M. , Blankenship Robert E. 
Published: June 2016

Significance
All photosynthetic organisms face the challenge of absorbing solar energy and regulating its flow through their light-harvesting antennas across widely varying photic conditions. For anoxygenic phototrophs, this process is complicated by the need to downregulate photosynthetic output when oxygen is encountered. The Fenna–Matthews–Olson protein from green sulfur bacteria is able to quench excitations in aerobic conditions effectively despite its apparent lack of photoprotective accessory molecules, indicating a previously unidentified type of energy transfer regulation. In this study, we provide evidence for a novel energy-quenching mechanism involving cysteine–bacteriochlorophyll photochemistry. This interaction should be able to be programed into other natural or bio-inspired antennas, opening new possibilities for regulating these systems in response to excess light.
Geospatial modeling approach to monument construction using Michigan from A.D. 1000–1600 as a case study
Authors: Howey Meghan C. L. , Palace Michael W. , McMichael Crystal H. 
Published: June 2016

Significance
Monumental construction was one way that past societies reconfigured their landscapes in response to social and environmental factors. Given that these factors changed through space and time, societies often constructed multiple types of monuments. We develop a maximum entropy modeling (MaxEnt) framework for identifying the spatioenvironmental factors that mattered most in the placement of different monument types. We turned to MaxEnt, given its ability to model spatial distributions from presence-only data. With modern development continuing to destroy archaeological sites across the globe, archaeological datasets, including monument locations, are evermore restricted to being presence-only data. Our framework shows how archaeologists can harness MaxEnt to develop robust models of past cultural processes, including monumentality, even when faced with limited, presence-only data.
Interbacterial signaling via
Burkholderia
contact-dependent growth inhibition system proteins
Authors: Garcia Erin C. , Perault Andrew I. , Marlatt Sara A. , Cotter Peggy A. 
Published: June 2016

Significance
How bacteria interact with one another has implications for human health and disease because complex bacterial communities like biofilms can impact agriculture, infection transmission, and disease progression. Contact-dependent growth inhibition systems are proteins produced by many bacteria that deliver toxins to neighboring bacteria, allowing the producing cell to inhibit competitors that do not make the correct antidote. Here, we show that these systems not only antagonize competitors but also mediate communication and cooperation between bacteria that produce identical toxin/antidote pairs. Antidote-containing bacteria that are targeted by toxins change their gene expression to promote biofilm formation. Leading to a more complete understanding of how these antibacterial protein systems function, this study will inform future development of therapeutics, vaccines, and decontaminants.
Diel Variations in Survey Catch Rates and Survey Catchability of Spiny Dogfish and their Pelagic Prey in the Northeast U.S. Continental Shelf Large Marine Ecosystem
Authors: Sagarese Skyler R. , Frisk Michael G. , Cerrato Robert M. , Sosebee Kathy A. , Musick John A. , Rago Paul J. 
Published: June 2016

Abstract
This study examines the potential uncertainty in survey biomass estimates of Spiny Dogfish Squalus acanthias in the Northeast U.S. Continental Shelf Large Marine Ecosystem (NES LME). Diel catch-per-unit-effort (CPUE) estimates are examined from the Northeast Fisheries Science Center bottom trawl surveys conducted during autumn (1963–2009) and spring (1968–2009). Influential environmental variables on survey catchability are identified for Spiny Dogfish life history stages and five pelagic prey species: Butterfish Peprilus triacanthus, Atlantic Herring Clupea harengus, shortfin squid Illex spp., longfin squid Doryteuthis spp., and Atlantic Mackerel Scomber scombrus. Daytime survey catchability was significantly higher than nighttime catchability for most species during autumn and for mature male Spiny Dogfish, shortfin squid, and longfin squid during spring in the NES LME. For most stages and species examined, breakpoint analyses identified significant increases in CPUE in the morning, peak CPUE during the day, and significant declines in CPUE in the late afternoon. Seasonal probabilities of daytime catch were largely driven by solar zenith angle for most species, with stronger trends identified during autumn. Unadjusted CPUE estimates appear to overestimate absolute abundance, with adjustments resulting in reductions in absolute abundance ranging from 41% for Spiny Dogfish to 91% for shortfin and longfin squids. These findings have important implications for Spiny Dogfish regarding estimates of population consumption of key pelagic prey species and their ecological footprint within the NES LME.
Received February 25, 2015; accepted December 16, 2015
A prospective picture collection study for a grading atlas of radiation dermatitis for clinical trials in head-and-neck cancer patients
Authors: Zenda Sadamoto , Ota Yosuke , Tachibana Hiroyuki , Ogawa Hirofumi , Ishii Shinobu , Hashiguchi Chikako , Akimoto Tetsuo , Ohe Yuichiro , Uchitomi Yosuke 
Published: June 2016

Abstract
Radiation dermatitis is one of the most common acute toxicities of both radiotherapy and chemoradiotherapy. Many clinical trials have evaluated the level of toxicity using the Common Terminology Criteria for Adverse Events ver. 4.03. This criterion accounts for severity in a single sentence only, and no visual classification guide has been available. Thus, there is a risk of subjective interpretation by the individual investigator. This contrasts with the situation with hematologic toxicities, which can be interpreted objectively. The aim of this prospective picture collection study was to develop a grading tool for use in establishing the severity of radiation dermatitis in clinical trials. A total of 118 patients who were scheduled to receive definitive or postoperative radiotherapy or chemoradiotherapy were enrolled from the four participating cancer centers. All researchers in our group used the same model of camera under the same shooting conditions to maintain consistent photographic quality. In all, 1600 photographs were collected. Of these, 100 photographs qualified for the first round of selection and were then graded by six experts, basically in accordance with the CTCAE ver. 4.03 (JCOG ver. in Japanese). After further study, 38 photographs were selected as representing typical models for Grade 1–4 radiation dermatitis; the radiation dermatitis grading atlas was produced from these photographs. The atlas will play a major role in ensuring that the dermatitis rating system is consistent between the institutions participating in trials. We hope that this will contribute to improving the quality of clinical trials, and also to improving the level of routine clinical practice.
Movement Disorders
Authors: Selwa Linda M. , Gelb Douglas J. 
Published: June 2016

Abstract
The term “movement disorder” refers to a heterogeneous group of conditions that result in abnormal form or timing of voluntary movement in individuals with normal strength and sensation. Movement disorders can be grouped into three general categories, hypokinetic, hyperkinetic, and ataxic. Hypokinetic movement disorders are characterized by tremors. Hyperkinetic movement disorders are characterized by involuntary movements that intrude into the normal flow of motor acts. Ataxic movement disorders are characterized by a lack of speed and skill in performing acts requiring the smoothly coordinated activity of several muscles.
Sleep Disorders
Authors: Gelb Douglas J. 
Published: June 2016

Abstract
Sleep consists of a highly patterned sequence of cyclic activity in various regions of the brain; it is not simply a state of temporary unconsciousness. Although the brain is less responsive than normal during sleep, it is not totally unresponsive. In fact, during sleep the brain responds more readily to meaningful stimuli. Rapid eye movement (REM) sleep can be characterized as a period when the brain is active and the body is paralyzed, whereas in nonrapid eye movement (NREM) sleep, the brain is less active but the body can move. Sleep disorders are grouped into three general categories, based on whether patients have trouble staying awake, trouble sleeping, or abnormal behaviors during sleep.
Dizziness and Disequilibrium
Authors: Gelb Douglas J. 
Published: June 2016

Abstract
Patients use the word “dizzy” in many different ways. It can refer to light- headedness, a sense of spinning or other movement, balance difficulty, clumsiness, confusion, or a vague sense of fogginess or malaise. The processes that affect the peripheral vestibular system are distinct from those that affect it centrally. Several features help to distinguish central from peripheral lesions. Patients with disequilibrium because of an inadequate motor response usually have difficulty maintaining their balance even with their eyes open.
The Electronic Health Record Objective Structured Clinical Examination: Assessing Student Competency in Patient Interactions While Using the Electronic Health Record
Authors: Biagioli Frances E. , Elliot Diane L. , Palmer Ryan T. , Graichen Carla C. , Rdesinski Rebecca E. , Ashok Kumar Kaparaboyna , Galper Ari B. , Tysinger James W. 
Published: June 2016

Problem
Because many medical students do not have access to electronic health records (EHRs) in the clinical environment, simulated EHR training is necessary. Explicitly training medical students to use EHRs appropriately during patient encounters equips them to engage patients while also attending to the accuracy of the record and contributing to a culture of information safety.

Approach
Faculty developed and successfully implemented an EHR objective structured clinical examination (EHR-OSCE) for clerkship students at two institutions. The EHR-OSCE objectives include assessing EHR-related communication and data management skills.

Outcomes
The authors collected performance data for students (n = 71) at the first institution during academic years 2011–2013 and for students (n = 211) at the second institution during academic year 2013–2014. EHR-OSCE assessment checklist scores showed that students performed well in EHR-related communication tasks, such as maintaining eye contact and stopping all computer work when the patient expresses worry. Findings indicated student EHR skill deficiencies in the areas of EHR data management including medical history review, medication reconciliation, and allergy reconciliation. Most students’ EHR skills failed to improve as the year progressed, suggesting that they did not gain the EHR training and experience they need in clinics and hospitals.

Next Steps
Cross-institutional data comparisons will help determine whether differences in curricula affect students’ EHR skills. National and institutional policies and faculty development are needed to ensure that students receive adequate EHR education, including hands-on experience in the clinic as well as simulated EHR practice.