bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective oxidation of aliphatic C–H bonds in alkylphenols by a chemomimetic biocatalytic system
Authors: Du Lei , Dong Sheng , Zhang Xingwang , Jiang Chengying , Chen Jingfei , Yao Lishan , Wang Xiao , Wan Xiaobo , Liu Xi , Wang Xinquan , Huang Shaohua , Cui Qiu , Feng Yingang , Liu Shuang-Jiang , Li Shengying 
Published: June 2017

SignificanceSelective oxidation of aliphatic C–H bonds in alkylphenols is important for both structural derivatization and biological degradation of these fundamental chemicals. However, significant problems are persistently associated with the chemical methods for this oxofunctionalization. In this study, we developed a unique chemomimetic biocatalytic system that is capable of selectively oxidizingp- andm-alkylated phenols in a controllable manner, overcoming the challenges faced by similar chemical oxidation. The structural and bioinformatics analyses of the central P450 biocatalyst CreJ suggest that its substrate flexibility and reaction selectivity could be further leveraged. This novel alkylphenol biooxidation system may hold great potential for application in pharmaceutical, biomanufacturing, and environmental industries once upscaled systems can be further developed in the future.
Trigger loop of RNA polymerase is a positional, not acid–base, catalyst for both transcription and proofreading
Authors: Mishanina Tatiana V. , Palo Michael Z. , Nayak Dhananjaya , Mooney Rachel A. , Landick Robert 
Published: June 2017

Significance
Synthesis of new RNA and removal of incorrect nucleotides during proofreading by RNA polymerase involve the transfer of two protons. Here, we show that a polymerase component, the trigger loop, does not directly mediate proton transfer during these reactions, as previously proposed. Instead, the trigger loop plays a central role in transcription as a positional catalyst, by orienting the reactants and promoting the polymerase backtracking necessary for proofreading. This positional-catalyst model of trigger-loop function explains its diverse effects on polymerase catalysis and reconciles contradictory reports in the literature. By establishing that the trigger loop is not an acid–base catalyst, our results also guide the search for alternative proton donors and acceptors for reactions in the active site of polymerase.
Bioengineered silkworms with butterfly cytotoxin-modified silk glands produce sericin cocoons with a utility for a new biomaterial
Authors: Otsuki Ryosuke , Yamamoto Masafumi , Matsumoto Erika , Iwamoto Shin-ichi , Sezutsu Hideki , Suzui Masumi , Takaki Keiko , Wakabayashi Keiji , Mori Hajime , Kotani Eiji 
Published: June 2017

Significance
Specific gene functions have been successfully suppressed by gene silencing or editing in many organisms. However, genetic manipulation to suppress the function of a target tissue has not been achieved using cytotoxin genes. We established transgenic silkworms with posterior silk glands (PSGs) that express the enzymatic domain of the cytotoxin pierisin-1A (P1A). The larvae with the modified PSGs produced the sericin cocoons with potential utilities in tissue engineering. The targeted P1A expression was found to cause site-specific repression of certain protein synthesis that appeared to have no impact on the developmental stages of individuals. Thus, the new approach through targeted P1A expression could be applicable to the development of biologically useful model organisms with tissue-specific dysfunction.
Retroviral host range extension is coupled with Env-activating mutations resulting in receptor-independent entry
Authors: Lounková Anna , Kosla Jan , Přikryl David , Štafl Kryštof , Kučerová Dana , Svoboda Jan 
Published: June 2017

Significance
The emergence of novel infectious diseases is often associated with cross-species virus transmission. Virus host range is owed, in large part, to genetic variation of its envelope gene. The illustrative example presented here is based on a structural study of the Rous sarcoma virus (RSV) avian retrovirus passaged twice through rodents. RSV heterotransmission was enabled by spontaneous envelope gene mutations, which allow virus entry even into human and other receptor-free cells. Through three independent biochemical assays, we established that these mutations caused conformational change similar to the one that follows virus–receptor interaction. The newly identified envelope mutations responsible for the broad retrovirus host range contribute to our understanding of retroviruses’ pathogenicity and their ability to cross the transclass barriers.
Maintenance of antiangiogenic and antitumor effects by orally active low-dose capecitabine for long-term cancer therapy
Authors: Zhang Yin , Sun Meili , Huang Guichun , Yin Linlin , Lai Qinghua , Yang Yunlong , Xing Xiaoming , Yu Guohua , Sun Yuping , Wang Xinsheng , Nie Guohui , Liu Yizhi , Cao Yihai 
Published: June 2017

Significance
Withdrawal of antiangiogenic drugs leads to tumor revascularization, even rebound effects of tumor angiogenesis, and potential metastasis. Long-term maintenance therapy with antiangiogenic drugs is crucial for achieving maximal clinical benefits for cancer patients. There are no antiangiogenic drugs that are clinically available for maintenance therapy. We show that orally active capecitabine at an extremely low and nontoxic dose displays a potent antiangiogenic effect that can be used for maintenance therapy. Importantly, the low-dose capecitabine in a sequentially therapeutic setting following anti-VEGF drugs produces remarkable anticancer effects. If successfully proven in clinical settings, our therapeutic regimen would be beneficial for millions of cancer patients. Our findings will shift the paradigm of current antiangiogenic therapy for treatment of human cancer patients.
Skin-specific regulation of SREBP processing and lipid biosynthesis by glycerol kinase 5
Authors: Zhang Duanwu , Tomisato Wataru , Su Lijing , Sun Lei , Choi Jin Huk , Zhang Zhao , Wang Kuan-wen , Zhan Xiaoming , Choi Mihwa , Li Xiaohong , Tang Miao , Castro-Perez Jose M. , Hildebrand Sara , Murray Anne R. , Moresco Eva Marie Y. , Beutler Bruce 
Published: June 2017

Significance
We discovered a previously unrecognized regulator of cholesterol biosynthesis, glycerol kinase 5 (GK5), which functions exclusively in the skin independently of cholesterol regulation in other tissues. GK5 negatively regulates the processing and nuclear localization of sterol regulatory element binding proteins, transcription factors that control expression of virtually all cholesterol synthesis enzymes. Excessive amounts of cholesterol, triglycerides, and ceramides were found in the skin of GK5-deficient mice. These mice displayed alopecia (hair loss) caused by impaired hair growth and maintenance, for which proper amounts of cholesterol and other skin lipids are necessary.
Structural studies of viperin, an antiviral radical SAM enzyme
Authors: Fenwick Michael K. , Li Yue , Cresswell Peter , Modis Yorgo , Ealick Steven E. 
Published: June 2017

SignificanceWe report structures of viperin, an antiviral radicalS-adenosylmethionine (SAM) enzyme. The overall structure shows a canonical radical SAM enzyme fold that harbors a [4Fe-4S] cluster. Structures with a bound SAM analog or SAM cleavage products are consistent with a conventional mechanism of radical formation. Sequence alignments guided by the putative active site residues of viperin reveal viperin-like enzymes in species from all kingdoms of life. Structural alignments show similarity between viperin and the molybdenum cofactor biosynthetic enzyme MoaA and show that the active site architecture of viperin is consistent with a nucleoside triphosphate substrate.
Prostaglandin E2 is essential for efficacious skeletal muscle stem-cell function, augmenting regeneration and strength
Authors: Ho Andrew T. V. , Palla Adelaida R. , Blake Matthew R. , Yucel Nora D. , Wang Yu Xin , Magnusson Klas E. G. , Holbrook Colin A. , Kraft Peggy E. , Delp Scott L. , Blau Helen M. 
Published: June 2017

Significance
Muscle repair after injury entails an immune response that orchestrates efficacious regeneration. Here we identify Prostaglandin E2 (PGE2) as a crucial inflammatory mediator of muscle stem cells (MuSCs), the building blocks of muscle regeneration. PGE2 is synthesized and secreted into the stem-cell niche in response to injury, leading to robust MuSC proliferation, key to myofiber repair. EP4 is the receptor that mediates PGE2 signaling in MuSCs, and genetically engineered mice that lack EP4 in MuSCs have impaired regeneration. Nonsteroidal anti-inflammatory drugs (NSAIDs), commonly used to treat pain after muscle injury, inhibit PGE2 synthesis, hinder muscle regeneration, and lead to weakened muscles. Importantly, a single treatment of injured muscles with PGE2 dramatically accelerates muscle repair and recovery of strength.
Dynamic maps of UV damage formation and repair for the human genome
Authors: Hu Jinchuan , Adebali Ogun , Adar Sheera , Sancar Aziz 
Published: June 2017

Significance
Nucleotide excision repair removes DNA damage caused by carcinogens, such as UV and anticancer drugs, such as cisplatin. We have developed two methods, high-sensitivity damage sequencing and excision repair sequencing that map the formation and repair of damage in the human genome at single-nucleotide resolution. The combination of dynamic damage and repair maps provides a holistic perspective of UV damage and repair of the human genome and has potential applications in cancer prevention and chemotherapy.
Broken flow symmetry explains the dynamics of small particles in deterministic lateral displacement arrays
Authors: Kim Sung-Cheol , Wunsch Benjamin H. , Hu Huan , Smith Joshua T. , Austin Robert H. , Stolovitzky Gustavo 
Published: June 2017

Significance
Deterministic lateral displacement (DLD) is a technique for size fractionation of particles in continuous flow that has shown great potential for biological and clinical applications. Several theoretical models have been proposed to explain the trajectories of different-sized particles in relation to the geometry of the pillar array, but experimental evidence has demonstrated that a rich class of intermediate migration behavior exists, which is not predicted by models. In this work, we present a unified theoretical framework to infer the trajectory of particles in the whole array on the basis of trajectories in the unit cell. This framework explains many of the unexpected particle trajectories reported in literature and can be used to design arrays for the fractionation of particles, even at the smallest scales reaching the molecular realm. We also performed experiments that verified our predictions, even at the nanoscales. Using our model as a set of design rules, we developed a condenser structure that achieves full particle separation with a single fluidic input.
Interface-induced multiferroism by design in complex oxide superlattices
Authors: Guo Hangwen , Wang Zhen , Dong Shuai , Ghosh Saurabh , Saghayezhian Mohammad , Chen Lina , Weng Yakui , Herklotz Andreas , Ward Thomas Z. , Jin Rongying , Pantelides Sokrates T. , Zhu Yimei , Zhang Jiandi , Plummer E. W. 
Published: June 2017

Significance
Developments in synthesis and characterizing artificially structured materials have greatly advanced the possibility to explore new states of matter in material science. Recent discoveries show that new quantum states can be achieved at heterointerfaces with various electric and mechanical boundary conditions. It remains an open question of how to design ultrathin layers with properties inaccessible in bulk phases that are amenable to technological applications. In this work, we grow heterostructures with extremely high-quality interfaces shown by state-of-the-art atomically resolved electron microscopy and spectroscopy. This combination allows us to identify an interface-induced structure that stabilizes ferromagnetism. Coupled with theory, we provide a conceptually useful recipe to design low-dimensional materials with unique functionalities, in line with the loop “make, measure, model.”
Hydroacoustic Assessment of Behavioral Responses by Fish Passing Near an Operating Tidal Turbine in the East River, New York
Authors: Bevelhimer Mark , Scherelis Constantin , Colby Jonathan , Adonizio Mary Ann 
Published: June 2017

AbstractAn important environmental issue facing the marine and hydrokinetic energy industry is whether fish that encounter underwater energy devices are likely to be struck and injured by moving components, primarily rotating turbine blades. The automated analysis of nearly 3 weeks of multibeam hydroacoustics data identified about 35,000 tracks of fish passing a tidal turbine in the East River, New York. These tracks included both individual fish and schools during periods with the turbine absent, the turbine present and operating, and the turbine present but not operating. The density of fish in the sampled area when the turbine was absent was roughly twice the density observed when the turbine was in place, particularly when the turbine was operating. This suggests that some avoidance occurred before fish were close enough to the turbine to be observed by the hydroacoustics system. Various measures of swimming behavior (direction, velocity, and linearity) were calculated for each track and evaluated for indication of behavioral responses to turbine presence and operation. Fish tracks were grouped based on tidal cycle, current velocity, and swimming direction and were evaluated with respect to turbine presence and operation and with respect to distance from the turbine. Nonparametric tests (Kolmogorov–Smirnov test) and multivariate analysis (canonical discriminant analysis) found significant differences among groups with respect to turbine presence and operation, suggesting that some fish responded to the turbine by adjusting swimming behavior, such as making small adjustments to swimming direction and velocity as they passed near the turbine. We found no evidence that fish were being struck by rotating blades, but there did appear to be large‐scale avoidance initiated out of the range of the hydroacoustics detection system. More study is needed to determine whether such avoidance behavior has significant ramifications for normal fish movement patterns, bioenergetics, seasonal migrations, and predator exposure.Received October 28, 2016; accepted May 29, 2017 Published online August 2, 2017
Ferulic acid and its water-soluble derivatives inhibit nitric oxide production and inducible nitric oxide synthase expression in rat primary astrocytes
Authors: Kikugawa Masaki , Ida Tomoaki , Ihara Hideshi , Sakamoto Tatsuji 
Published: June 2017

Abstract
We recently reported that two water-soluble derivatives of ferulic acid (1-feruloyl glycerol, 1-feruloyl diglycerol) previously developed by our group exhibited protective effects against amyloid-β–induced neurodegeneration in vitro and in vivo. In the current study, we aimed to further understand this process by examining the derivatives’ ability to suppress abnormal activation of astrocytes, the key event of neurodegeneration. We investigated the effects of ferulic acid (FA) derivatives on nitric oxide (NO) production and inducible nitric oxide synthase (iNOS) expression in rat primary astrocytes. The results showed that these compounds inhibited NO production and iNOS expression in a concentration-dependent manner and that the mechanism underlying these effects was the suppression of the nuclear factor-κB pathway. This evidence suggests that FA and its derivatives may be effective neuroprotective agents and could be useful in the treatment of neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease.
GfaPy: a flexible and extensible software library for handling sequence graphs in Python
Authors: Gonnella Giorgio , Kurtz Stefan 
Published: June 2017

Abstract

Summary
GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Here, we present GfaPy, a software package for creating, parsing and editing GFA graphs using the programming language Python. GfaPy supports GFA 1 and GFA 2, using the same interface and allows for interconversion between both formats. The software package provides a simple interface for custom record types, which is an important new feature of GFA 2 (compared to GFA 1). This enables new applications of the format.

Availability and implementation
GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pain Catastrophizing Moderates Relationships between Pain Intensity and Opioid Prescription
Authors: Sharifzadeh Yasamin , Kao Ming-Chih , Sturgeon John A. , Rico Thomas J. , Mackey Sean , Darnall Beth D. 
Published: June 2017

Abstract

Background
Pain catastrophizing is a maladaptive response to pain that amplifies chronic pain intensity and distress. Few studies have examined how pain catastrophizing relates to opioid prescription in outpatients with chronic pain.

Methods
The authors conducted a retrospective observational study of the relationships between opioid prescription, pain intensity, and pain catastrophizing in 1,794 adults (1,129 women; 63%) presenting for new evaluation at a large tertiary care pain treatment center. Data were sourced primarily from an open-source, learning health system and pain registry and secondarily from manual review of electronic medical records. A binary opioid prescription variable (yes/no) constituted the dependent variable; independent variables were age, sex, pain intensity, pain catastrophizing, depression, and anxiety.

Results
Most patients were prescribed at least one opioid medication (57%; n = 1,020). A significant interaction and main effects of pain intensity and pain catastrophizing on opioid prescription were noted (P < 0.04). Additive modeling revealed sex differences in the relationship between pain catastrophizing, pain intensity, and opioid prescription, such that opioid prescription became more common at lower levels of pain catastrophizing for women than for men.

Conclusions
Results supported the conclusion that pain catastrophizing and sex moderate the relationship between pain intensity and opioid prescription. Although men and women patients had similar Pain Catastrophizing Scale scores, historically “subthreshold” levels of pain catastrophizing were significantly associated with opioid prescription only for women patients. These findings suggest that pain intensity and catastrophizing contribute to different patterns of opioid prescription for men and women patients, highlighting a potential need for examination and intervention in future studies.
Cancer in pregnancy: safety and efficacy of systemic therapies
Authors: Boere Ingrid , Lok Christianne , Vandenbroucke Tineke , Amant Frédéric 
Published: June 2017

Purpose of review
Cancer in pregnancy has become increasingly frequent. It has become clear that for specific cancers under well defined circumstances, oncological treatment in pregnancy can be well tolerated and feasible for both mother and fetus. Continued critical assessment of the available literature and registration of cancer in pregnancy cases and outcomes for mother and child are necessary to work toward implementing optimal cancer treatment during pregnancy.

Recent findings
Physiologic changes in pregnancy may alter distribution and efficacy of systemic therapy. Data on systemic therapy including, chemotherapy, hormonal therapy, and targeted therapy during pregnancy are available but incomplete. Outcomes of fetuses exposed to chemotherapy in utero are generally reassuring, but new targeted therapies are mostly discouraged in pregnancy.

Summary
Cancer treatment during pregnancy is possible, depending on type and timing of systemic therapy and treatment modality. Available data are reassuring with a modest increase in complications such as growth restriction and preterm birth. The effect of new targeted therapies is often still unclear and therefore discouraged.
Cutaneous Collagenous Vasculopathy: Report of Two Cases Presenting as Disseminated Telangiectasias and Review of the Literature
Authors: Bondier Laure , Tardieu Mathilde , Leveque Perrine , Challende Isabelle , Pinel Nicole , Leccia Marie T. 
Published: June 2017

Abstract:
Cutaneous collagenous vasculopathy is a recently described idiopathic microangiopathy characterized by acquired diffuse cutaneous telangiectasias and specific histological features: dilated capillaries in the superficial dermis, with walls thickened by hyaline material containing collagen IV by immunohistochemistry. The authors describe 2 cases and review all cases reported in the literature to date, 34 cases including our own. Cases were mainly observed in women (sex ratio 0.41), median age 63.5 (16–85). Hypertension and diabetes seem more frequent in these patients than in the general population. Typical clinical presentation is fine hair telangiectasias appearing on the lower limbs and progressing toward the trunk and upper limbs, sparing the face. Facial and neck involvement are however reported. When faced with isolated acquired diffuse cutaneous telangiectasias, clinicians should perform a skin biopsy to rule out cutaneous collagenous vasculopathy.
Phosphohistone-H3 and Ki67: Useful Markers in Differentiating Dermatofibroma From Dermatofibrosarcoma Protuberans and Atypical Fibrohistiocytic Lesions
Authors: Agarwal Atin , Gopinath Arun , Tetzlaff Michael T. , Prieto Victor G. 
Published: June 2017

Abstract:
Dermatofibromas (DF) are common, benign, skin tumors, usually easily differentiated from dermatofibrosarcoma protuberans (DFSP) by the presence of a relative low cellularity, lesser degree of infiltration of subcutaneous tissue, and immunohistochemical pattern (eg, FXIIIa in DF and CD34 in DFSP). Atypical fibrohistiocytic lesions (AFL) have features intermediate to DF and DFSP (trunk location, storiform pattern, infiltration of the subcutaneous tissue, and focal expression of both CD34 and Factor XIIIa). It is unclear if mitotic counts/degree of proliferation is helpful to distinguish DF from DFSP. To study the mitotic rate and proliferation index in DF, AFL/DFSP, anti-ki67, and anti-PHH3 were performed on 10 cases of DF (including 4 cellular DF), 10 standard DFSP, and 2 AFL. The proliferation index and mitotic figures were counted per square millimeter in a “hotspot” (in a fashion similar to mitotic counts in melanoma). All cases of DF showed much higher Ki67 proliferation index (P = 0.0001) along with increased mitotic figures both on H&E and with anti-PHH3 (P = 0.0001) when compared to AFL/DFSP. Our data indicate that DF has a higher proliferation index and mitotic counts when compared to superficial/peripheral portion of AFL and DFSP. This finding may be helpful in the differential diagnosis among these fibrohistiocytic lesions.
Plaque-Like Pilar Sheath Acanthoma: Histopathologic and Immunohistochemical Study of 3 Unusual Cases
Authors: Jo-Velasco Margarita , Corrales-Rodríguez Araceli , Francés-Rodríguez Laura , Alegría-Landa Victoria , Eraña-Tomás Itziar , Rütten Arno , Requena Luis 
Published: June 2017

Abstract:
Pilar sheath acanthoma is an uncommon, benign follicular neoplasm that frequently presents as a solitary lesion. This neoplasm usually appears on the skin around the upper lip of elderly patients. Histopathologically, the neoplasm usually shows a cystic configuration with epithelial lobules resembling to those of the outer root sheath of the hair follicle at the level of the isthmus emanating radially from the cyst wall. We present 3 peculiar cases of a pilar sheath acanthoma showing a plaque-like architecture because the lesions exhibited a horizontal configuration. To our knowledge, there are no previously reported examples of plaque-like pilar sheath acanthoma.