bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal Ultra Short Photodynamic Therapy: Heating Fibroblasts During Sub–30-Minute Incubation of 5-Aminolevulinic Acid Increases Photodynamic Therapy–Induced Cell Death
Authors: Koo Eugene , Austin Evan , Mamalis Andrew , Jagdeo Jared 
Published: October 2017

BACKGROUND
Actinic keratoses (AKs) prevalence was estimated at 39.5 million Americans in 2004, and the cost to treat AKs that year was approximately 1 billion dollars. Photodynamic therapy (PDT) is an FDA-approved therapy for the treatment of AK. Recent studies have focused on reducing PDT treatment time while maintaining efficacy.

OBJECTIVE
To investigate the use of thermal modulation to improve the efficacy of ultra short aminolevulinic acid (ALA) incubation PDT.

MATERIALS AND METHODS
Human dermal fibroblasts (HDFs) were incubated for 10, 15, or 20 minutes with 0.5-mM ALA at various temperatures (21, 24, 27, 30, 33, 36, 39, and 42°C). After ALA incubation, samples were treated for 1,000 seconds with blue light (417 ± 5 nm) resulting in a fluence of 10 J/cm2. Samples were collected and stained for apoptosis/necrosis with annexin-V and 7-aminoactinomycin D (7-AAD), then analyzed by flow cytometry.

RESULTS
Human dermal fibroblast treated with 10-minute ALA-PDT had no statistically significant changes in apoptosis at all temperatures. Human dermal fibroblast treated with 15- or 20-minute ALA-PDT had statistically significant increases in apoptosis at 39 and 42°C (p < .05).

CONCLUSION
These results suggest the use of thermal modulation may improve ultra short ALA incubation PDT efficacy.
Comparison of Moderate and High Energy of a Nano-Fractional Radiofrequency Treatment on a Photoaging Hairless Mice Model
Authors: Sun Wenjia , Zhang Chengfeng , Zhao Juemin , Wu Jiaqiang , Xiang Leihong 
Published: October 2017

BACKGROUND
Fractional radiofrequency (FRF) has been widely used in skin rejuvenation. To explore optimal settings, it is important to compare different treatment parameters.

OBJECTIVE
This study was designed to compare the effect of moderate-energy and high-energy FRF treatment on a hairless mice model.

METHODS
Fifteen photoaged hairless mice were assigned to 3 groups: control, moderate energy, and high energy. Two treatment sessions (T × 1 and T × 2) were performed at 1-month interval. Transepidermal water loss was measured at baseline, immediately, 1, 2, and 4 weeks after T × 1. Skin samples were harvested before each treatment, 1 and 2 months after T × 2. Neocollagenesis was evaluated by hematoxylin and eosin staining, Masson staining, and immunohistochemistry analysis.

RESULTS
Transepidermal water loss of high-energy group was significantly higher than the moderate-energy group (p = .008) immediately after T × 1. Remarkable fibroblast proliferation was observed at 1 month after T × 1, followed by significant dermal thickening, and increase of Type I collagen and Type III collagen. There was no significant difference between 2 energy groups in fibroblast proliferation, dermal thickness, and collagen density.

CONCLUSION
The effect of moderate-energy treatment was comparable with that of high energy in neocollagenesis, whereas moderate energy yielded less damage to skin barrier function.
Bacterial Keratitis: Isolated Organisms and Antibiotic Resistance Patterns in San Francisco
Authors: Peng Michelle Y. , Cevallos Vicky , McLeod Stephen D. , Lietman Thomas M. , Rose-Nussbaumer Jennifer 
Published: October 2017

Purpose:
Understanding the spectrum of pathogens in a given geographic region is important when deciding on empiric antibiotic therapy. In this study, we evaluate the spectrum of bacterial organisms cultured from corneal samples and their antibiotic sensitivities to guide initial treatment of keratitis.

Methods:
We performed a retrospective case review of cultures from suspected infectious keratitis cases at the Francis I. Proctor Foundation, University of California, San Francisco, from 1996 through 2015. Logistic regression models were used to assess the risk of culturing methicillin-resistant Staphylococcus aureus (MRSA) from ulcers over time and the association between the year cultured and moxifloxacin resistance.

Results:
A total of 522 of 2203 (23.7%) cultures grew bacterial organisms believed to be the etiology of infection, with available antibiotic sensitivity data. Of these, 338 (65.3%) grew gram-positive organisms with the most common being methicillin-sensitive Staphylococcus aureus (20.1%, N = 105). One hundred eighty (34.7%) grew gram-negative species with Pseudomonas aeruginosa as the most prevalent organism (10.9%, N = 57). There was 1.13 increased odds of culturing MRSA for each 1-year increase in the culture date (P = 0.01) and 1.26 increased odds of culturing an organism resistant to moxifloxacin with each 1-year increase in the culture date after controlling for the infectious organism (P < 0.001).

Conclusions:
Gram-positive organisms are the most commonly identified etiology of microbial keratitis in this series. Approximately 35% of cultured organisms had variable susceptibility to moxifloxacin, and resistance seems to be increasing over time. The risk of culturing MRSA increased over time.
Recognizing and Managing Bullous Descemet Detachment Secondary to Accidental Hydroseparation During Phacoemulsification/Cataract Surgery by Relaxing Descemetotomy
Authors: Jacob Soosan , Agarwal Amar , Agarwal Athiya , Ai Saijimol 
Published: October 2017

Purpose:
To report a new technique called relaxing Descemetotomy for treatment of bullous Descemet detachment (BDD) secondary to accidental hydroseparation of Descemet membrane (DM) during stromal hydration in cataract surgery.

Methods:
A clear corneal keratome entry was created close to the limbus extending inward to create a relaxing cut (ab externo relaxing Descemetotomy) on taut DM, thus creating an egress route for supra-Descemetic fluid (SDF). This was followed by pneumodescemetopexy to drain SDF internally.

Results:
Three patients with a history of unsuccessful pneumodescemetopexy and with planar or mildly convex separation of DM without break on anterior segment optical coherence tomography (ASOCT) underwent this procedure. All had successful reapposition of DM clinically and on ASOCT. All showed resolution of stromal edema and improved uncorrected and best-corrected visual acuity postoperatively.

Conclusions:
Rarely stromal hydration performed with an irrigating cannula positioned too close to the posterior stroma can result in hydroseparation of DM creating BDD, seen intraoperatively as a fluid wave propagating across the posterior aspect of the cornea. Large folds, free mobility, and DM tear classically seen with rhegmatogenous Descemet detachment are not seen clinically or on ASOCT in BDD. Pneumodescemetopexy alone cannot resolve BDD because without a DM tear, SDF cannot evacuate. Combining relaxing Descemetotomy with pneumodescemetopexy allows SDF to drain internally and Descemet detachment to resolve. This technique has numerous advantages over classical venting incisions in terms of ease, preferable limbal location, larger incision size, absence of complications such as visual axis scars, irregular astigmatism, epithelial ingrowth, infectious keratitis, etc.
Molecular Typing and Macrolide Resistance of Syphilis Cases in Manitoba, Canada, From 2012 to 2016
Authors: Shuel Michelle , Hayden Kristy , Kadkhoda Kamran , Tsang Raymond S.W. 
Published: October 2017

Background
The province of Manitoba, Canada, with a population of approximately 1.3 million, has been experiencing increased incidence of syphilis cases since 2015. In this study, we examined the detection of Treponema pallidum DNA in 354 clinical samples from 2012 to 2016, and determined molecular types and mutations conferring resistance to azithromycin in the polymerase chain reaction (PCR)–positive samples.

Methods

T. pallidum DNA detection was done by PCR amplification of tpp47, bmp, and polA genes. Syphilis serology results were reviewed for the PCR-positive cases. Molecular typing of syphilis strains was done by analysis of the T, pallidum arp, tpr, and tp0548 gene targets as well as partial sequencing of the 23S rRNA gene for azithromycin resistance.

Results
Of the 354 samples tested, 74 individual cases were PCR positive. A result from the treponemal antibody chemiluminescent microparticle immunoassay test was positive in 72 of these cases and that from the Venereal Disease Research Laboratory testing was positive in 66. Mutations conferring resistance to azithromycin were found in all 74 PCR-positive samples. Molecular typing was completed on 57 PCR-positive samples, and 12 molecular types were identified with 14d/g found in 63.2%. Increased strain diversity was observed with 8 molecular types detected in 2016, whereas only 2 to 3 types were found in 2012 to 2014. A patient with 2 episodes of infection 9 months apart caused by different molecular strain types was also identified.

Conclusions
The finding of an increase in genetic diversity in the strains in this study and an increase in macrolide resistance compared with previous Canadian reports highlighted the need for continued surveillance including strain characterization.
A CRISPR-Cas9 Genome Engineering Platform in Primary CD4+ T Cells for the Interrogation of HIV Host Factors
Authors: Hultquist Judd F. , Hiatt Joseph , Schumann Kathrin , McGregor Michael J. , Roth Theodore L. , Haas Paige , Doudna Jennifer , Marson Alexander , Krogan Nevan J. 
Published: October 2017

ABSTRACTCRISPR-Cas9 gene editing strategies have revolutionized our ability to engineer the human genome for robust functional interrogation of complex biological processes. We have recently adapted this technology to primary human T cells to generate a high-throughput platform for analyzing the role of host factors in pathogen infection and lifecycle. Here, we describe applications of this system to investigate HIV pathogenesis in CD4+ T cells. Briefly, CRISPR-Cas9 ribonucleoproteins (crRNPs) are synthesized in vitro and delivered to activated primary human CD4+ T cells by nucleofection. These edited cells are then validated and expanded for use in downstream cellular, genetic, or protein-based assays. Our platform supports the arrayed generation of several gene manipulations in only a few hours’ time and is widely adaptable across culture conditions, infection protocols, and downstream applications. We present detailed protocols for crRNP synthesis, primary T cell culture, 96-well nucleofection, molecular validation, and HIV infection with additional considerations for guide and screen design as well as crRNP multiplexing.
Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)
Authors: Bayona-Vásquez Natalia J , Glenn Travis C , Kieran Troy J , Pierson Todd W , Hoffberg Sandra L , Scott Peter A , Bentley Kerin E , Finger John W , Louha Swarnali , Troendle Nicholas , Díaz-Jaimes Píndaro , Mauricio Rodney , Faircloth Brant C 
Published: October 2017

AbstractMolecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially due to the inability to highly-multiplex samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that relies on adapters and primers designed inAdapterama I. Major features of our method include: 1) minimizing the number of processing steps; 2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; 3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; 4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; 5) interchangeable adapter designs; 6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; 7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, 8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
A molecular network of the aging brain implicatesINPPL1andPLXNB1in Alzheimer’s disease
Authors: Mostafavi S. , Gaiteri C. , Sullivan S. E. , White C.C. , Tasaki S. , Xu J. , Taga M. , Klein H. , Patrick E. , Komashko V. , McCabe C. , Smith R. , Bradshaw E.B. , Root D. , Regev A. , Yu L. , Chibnik L.B. , Schneider J.A. , Young-Pearse T. , Bennett D.A. , De Jager P.L. 
Published: October 2017

AbstractThe fact that only symptomatic therapies of small effect are available for Alzheimer’s disease (AD) today highlights the need for new therapeutic targets with which to prevent a major contributor to aging-related cognitive decline. Here, we report the construction and validation of a molecular network of the aging human frontal cortex. Using RNA sequence data from 478 individuals, we first identify the role of modules of coexpressed genes, and then confirm them in independent AD datasets. Then, we prioritize influential genes in AD-related modules and test our predictions in human model systems. We functionally validate two putative regulator genes in human astrocytes:INPPL1andPLXNB1, whose activity in AD may be related to semaphorin signalling and type II diabetes, which have both been implicated in AD. This arc of network identification followed by statistical and experimental validation provides specific new targets for therapeutic development and illustrates a network approach to a complex disease.One sentence summaryMolecular network analysis of RNA sequencing data from the aging human cortex identifies new Alzheimer’s and cognitive decline genes.
Enhanced intestinal reabsorption due to reduced metabolism of ceftriaxone
Authors: Sar Tapas K , Samanta Indranil , Hansda Rabindra N , Buragohain Rinku , Mandal Tapan K 
Published: October 2017

AbstractThe polyherbal drug (Fibrosin®) is often used as supportive therapy with intramuscular ceftriaxone injection for treatment of mastitis. A single dose of ceftriaxone at 50 mg kg−1was administered intramuscularly in six healthy lactating goats and a single oral dose of Fibrosin®(1.9 gm) was given 1 hr prior to intramuscular ceftriaxone injection to study disposition of ceftriaxone. Plasma and urine samples were collected at predetermined time schedule and ceftriaxone/ceftizoxime was extracted and analyzed by HPLC. Ceftriaxone persisted for 3 hr in plasma of fibrosin treated healthy lactating goats. Mean t½K (distribution half life) following absorption phase and t½K′(elimination half life) following intestinal re-absorption phase were respectively, 0.091 ± 0.01 and 0.43 ± 0.03 hr with a re-absorption half life (t½Ka′) of 0.18 ± 0.003 hr.Ceftriaxone at a lower concentration (67.91 ± 9.42 μg ml−1) was recovered at 24 hr post dosing from urine. This is the first report of pharmacokinetic interaction of intramuscular ceftriaxone injection and the oral polyherbal drug (which was found to be a cytochrome P450inhibitor).
Multiple interactions between Scc1 and Scc2 activate cohesin’s DNA dependent ATPase and replace Pds5 during loading
Authors: Petela Naomi J , Gligoris Thomas G , Metson Jean , Lee Byung-Gil , Voulgaris Menelaos , Hu Bin , Kikuchi Sotaro , Chapard Christophe , Chen Wentao , Rajendra Eeson , Srinivisan Madhusudhan , Yu Hongtao , Löwe Jan , Nasmyth Kim A 
Published: October 2017

SummaryIn addition to sharing with condensin an ability to organize DNA into chromatids, cohesin regulates enhancer-promoter interactions and confers sister chromatid cohesion. Association with chromosomes is regulated by hook-shaped HEAT repeat proteins that Associate With its Kleisin (Scc1) subunit (HAWKs), namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently displaces Pds5 during loading. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesin’s ATPase activity, loading, and translocation while Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesin’s initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2’s association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states, one with Pds5 bound to Scc1 that is not able to hydrolyse ATP efficiently but is capable of release from chromosomes and another in which Scc2, transiently replacing Pds5, stimulates the ATP hydrolysis necessary for loading and translocation away from loading sites.
COPD lungs show an attached stratified mucus layer resembling the protective colonic mucus
Authors: Fernández-Blanco Joan Antoni , Arike Liisa , Ermund Anna , Fakih Dalia , Rodríguez-Piñeiro Ana M. , Martínez-Abad Beatriz , Skansebo Elin , Jackson Sonya , Root James , Singh Dave , McCrae Christopher , Evans Christopher M. , Åstrand Annika , Hansson Gunnar C. 
Published: October 2017

AbstractThe respiratory tract is normally kept essentially free of bacteria by cilia-mediated mucus transport, but in chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF) mucus accumulates due to goblet cell hyperplasia and mucin overexpression. To address mechanisms behind the mucus accumulation, the elastase-induced mouse model was utilized. The proteomes of bronchoalveolar lavage fluid from elastase-induced mice and COPD patients showed similarities to each other and to colonic mucus. Lung mucus showed a striated, laminated appearance in the elastase-induced mice, COPD and CF, resembling that observed for colonic mucus. Less mucus obstruction was observed in mice lacking the Muc5b mucin. The accumulated mucus plugs of the elastase-induced mice were possible to wash out, but a mucus layer covering the epithelium remained attached to the surface goblet cells also after hypertonic saline washings as widely used in CF therapy. The results suggest that the lung can convert its mucus system into an attached mucus layer that protects the epithelium, similarly to the colon.
Genetic analysis ofde novovariants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicatesMYRFas a candidate gene
Authors: Qi Hongjian , Yu Lan , Zhou Xueya , Kitaygorodsky Alexander , Wynn Julia , Zhu Na , Aspelund Gudrun , Lim Foong Yen , Crombleholme Timothy , Cusick Robert , Azarow Kenneth , Danko Melissa Ellen , Chung Dai , Warner Brad W. , Mychaliska George B. , Potoka Douglas , Wagner Amy J. , ElFiky Mahmoud , Nickerson Deborah A. , Bamshad Michael J. , Wilson Jay M. , High Frances A. , Longoni Mauro , Donahoe Patricia , Chung Wendy K. , Shen Yufeng 
Published: October 2017

AbstractCongenital diaphragmatic hernia (CDH) is one of the most common and lethal birth defects. Previous studies using exome sequencing support a significant contribution of codingde novovariants in complex CDH cases with additional anomalies and likely gene-disrupting (LGD) variants in isolated CDH cases. To further investigate the genetic architecture of CDH, we performed exome or genome sequencing in 283 proband-parent trios. Combined with data from previous studies, we analyzed a total of 357 trios, including 148 complex and 209 isolated cases. Complex and isolated cases both have a significant burden of deleteriousde novocoding variants (1.7~fold, p= 1.2×10−5for complex, 1.5~fold, p= 9.0×10−5for isolated). Strikingly, in isolated CDH, almost all of the burden is carried by female cases (2.1~fold, p=0.004 for likely gene disrupting and 1.8~fold, p= 0.0008 for damaging missense variants); whereas in complex CDH, the burden is similar in females and males. Additionally,de novoLGD variants in complex cases are mostly enriched in genes highly expressed in developing diaphragm, but distributed in genes with a broad range of expression levels in isolated cases. Finally, we identified a new candidate risk geneMYRF(4de novovariants, p-value=2×10−10), a transcription factor intolerant of mutations. Patients withMYRFmutations have additional anomalies including congenital heart disease and genitourinary defects, likely representing a novel syndrome.
Human pluripotent reprogramming with CRISPR activators
Authors: Weltner Jere , Balboa Diego , Katayama Shintaro , Bespalov Maxim , Krjutškov Kaarel , Jouhilahti Eeva-Mari , Trokovic Ras , Kere Juha , Otonkoski Timo 
Published: October 2017

AbstractCRISPR/Cas9 based gene activation (CRISPRa) is an attractive tool for cellular reprogramming applications due to its high multiplexing capacity and direct targeting of endogenous loci. Here we present the reprogramming of primary human skin fibroblasts into induced pluripotent stem cells (iPSC) using CRISPRa, targeting endogenous OCT4, SOX2, KLF4, MYC and LIN28A promoters. The basal reprogramming efficiency can be improved by an order of magnitude by additionally targeting a conserved Alu-motif, enriched near genes involved in embryo genome activation (EEA-motif). This effect is mediated in part by more efficient activation of NANOG and REX1. These data constitute a proof of principle that somatic cells can be reprogrammed into iPSC using only CRISPRa. Furthermore, the results unravel previously uncharacterized involvement of EEA-motif-associated mechanisms in cellular reprogramming.