bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid, Selection-Free, High-Efficiency Genome Editing in Protozoan Parasites Using CRISPR-Cas9 Ribonucleoproteins
Authors: Soares Medeiros Lia Carolina , South Lilith , Peng Duo , Bustamante Juan M. , Wang Wei , Bunkofske Molly , Perumal Natasha , Sanchez-Valdez Fernando , Tarleton Rick L. 
Published: November 2017

ABSTRACT

Trypanosomatids (order Kinetoplastida), including the human pathogens
Trypanosoma cruzi
(agent of Chagas disease),
Trypanosoma brucei
, (African sleeping sickness), and
Leishmania
(leishmaniasis), affect millions of people and animals globally.
T. cruzi
is considered one of the least studied and most poorly understood tropical disease-causing parasites, in part because of the relative lack of facile genetic engineering tools. This situation has improved recently through the application of clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas9) technology, but a number of limitations remain, including the toxicity of continuous Cas9 expression and the long drug marker selection times. In this study, we show that the delivery of ribonucleoprotein (RNP) complexes composed of recombinant Cas9 from
Staphylococcus aureus
(SaCas9), but not from the more routinely used
Streptococcus pyogenes
Cas9 (SpCas9), and
in vitro
-transcribed single guide RNAs (sgRNAs) results in rapid gene edits in
T. cruzi
and other kinetoplastids at frequencies approaching 100%. The highly efficient genome editing via SaCas9/sgRNA RNPs was obtained for both reporter and endogenous genes and observed in multiple parasite life cycle stages in various strains of
T. cruzi
, as well as in
T. brucei
and
Leishmania major
. RNP complex delivery was also used to successfully tag proteins at endogenous loci and to assess the biological functions of essential genes. Thus, the use of SaCas9 RNP complexes for gene editing in kinetoplastids provides a simple, rapid, and cloning- and selection-free method to assess gene function in these important human pathogens.

IMPORTANCE
Protozoan parasites remain some of the highest-impact human and animal pathogens, with very limited treatment and prevention options. The development of improved therapeutics and vaccines depends on a better understanding of the unique biology of these organisms, and understanding their biology, in turn, requires the ability to track and manipulate the products of genes. In this work, we describe new methods that are available to essentially any laboratory and applicable to any parasite isolate for easily and rapidly editing the genomes of kinetoplastid parasites. We demonstrate that these methods provide the means to quickly assess function, including that of the products of essential genes and potential targets of drugs, and to tag gene products at their endogenous loci. This is all achieved without gene cloning or drug selection. We expect this advance to enable investigations, especially in
Trypanosoma cruzi
and
Leishmania
spp., that have eluded investigators for decades.
Different Substrate Preferences Help Closely Related Bacteria To Coexist in the Gut
Authors: Louis Petra 
Published: November 2017

ABSTRACT

Many factors shape the ability of different microbes to coexist in microbial communities. In the human gut, dietary and host-derived nutrients largely drive microbial community structure. How gut microbes with very similar nutrient profiles are able to coexist over time within the same host is not fully understood. Tuncil et al. (mBio 8:e01068-17, 2017,
https://doi.org/10.1128/mBio.01068-17
) explored glycan prioritization in two closely related human gut bacteria,
Bacteroides ovatus
and
Bacteroides thetaiotaomicron
, on complex glycan mixtures that both organisms can degrade. Determining depletion of the individual glycans over time in pure cultures and cocultures revealed that the bacteria seem to have hardwired differences in their preferences for different glycans which likely contribute to their stable coexistence. The researchers also established that gene expression changes of the corresponding polysaccharide utilization loci did not always mirror glycan depletion, which highlights that additional regulatory mechanisms must be present.
Cystic fibrosis newborn screening: outcome of infants with normal sweat tests
Authors: Edmondson Claire , Grime Christopher , Prasad Ammani , Cowlard Jacqui , Nwokoro Chinedu E C , Ruiz Gary , Wallis Colin , Balfour-Lynn Ian M 
Published: November 2017

Newborn babies positively screened for cystic fibrosis (CF) (high serum immunoreactive trypsin (IRT) with DNA analysis) are referred for a diagnostic sweat test, which may be normal (sweat chloride <30 mmol/L). Unless two gene mutations are identified during Newborn screening (NBS), the babies are discharged from follow-up. We wished to check that none had subsequently developed symptoms suggestive of CF. We retrospectively reviewed patient notes and contacted general practitioners of all babies with a negative sweat test, conducted in one of the four paediatric specialist CF centres in London, over the first 6 years of screening in South East England.Of 511 babies referred, 95 (19%) had a normal sweat test. Five (5%) had CF diagnosed genetically, two of them on extended genome sequencing after clinical suspicion. Eleven (12%) were designated as CF screen positive inconclusive diagnosis (CFSPID); one of the five CF children was originally designated as CFSPID. Seventy-nine (83%) were assumed to be false-positive cases and discharged; follow-up data were available for 51/79 (65%); 32/51 (63%) had no health issues, 19/51 (37%) had other significant non-CF pathology.These results are reassuring in that within the limitations of those lost to follow-up, CF symptoms have not emerged in the discharged children. The high non-CF morbidity in these children may relate to known causes of high IRT at birth. Clinicians need to be aware that a child can have CF despite a normal sweat test following NBS, and if symptoms suggest the diagnosis, further testing, including extended genome sequencing, is required.
Elevated mortality among weekend hospital admissions is not associated with adoption of seven day clinical standards
Authors: Meacock Rachel , Sutton Matt 
Published: November 2017

IntroductionPatients admitted to hospital in an emergency at weekends have been found to experience higher mortality rates than those admitted during the week. The National Health Service (NHS) in England has introduced four priority clinical standards for emergency hospital care with the objective of reducing deaths associated with this ‘weekend effect’. This study aimed to determine whether adoption of these clinical standards is associated with the extent to which weekend mortality is elevated.MethodsWe used publicly available data on performance against the four priority clinical standards in 2015 and estimates of Trusts’ weekend effects between 2013/2014 and 2015/2016 for 123 NHS Trusts in England. We examined whether adoption of the priority clinical standards was associated with the extent to which weekend mortality was elevated, and changes over a 3 year period in the extent to which mortality was elevated.ResultsLevels of achievement of two of the four clinical standards (ongoing review and access to diagnostic services) had small positive associations with the magnitude of the weekend effect in 2015/2016. Levels of achievement of the remaining two standards (time to first consultant review and access to consultant directed interventions) had small negative associations with the magnitude of the weekend effect in 2015/2016. No association was statistically significant. The same pattern was observed in the associations between achievement of the standards and changes in the magnitudes of the weekend effect between 2013/2014 and 2015/2016.DiscussionWe found no association between Trusts’ performance against any of the four standards and the current magnitude of their weekend effects, or the change in their weekend effects over the past 3 years. These findings cast doubt on whether adoption of seven day clinical standards in the delivery of emergency hospital services will be successful in reducing the weekend effect.
Condom use behaviour among people living with HIV: a seven-country community-based participatory research in the Asia-Pacific region
Authors: Deuba Keshab , Kohlbrenner Verena , Koirala Sushil , Ekström Anna Mia 
Published: November 2017

ObjectivesWe examined the prevalence of inconsistent condom use and its correlates among people living with HIV (PLHIV) in the Asia-Pacific region.MethodsBetween 1 October 2012 and 31 May 2013, a total of 7843 PLHIV aged 18–50 years were recruited using targeted and venue-based sampling in Bangladesh, Indonesia, Lao People’s Democratic Republic (PDR), Nepal, Pakistan, Philippines and Vietnam. Logistic regression was used to explore the association between condom use behaviour and demographics, social support, stigma and discrimination and various health-related variables.ResultsOverall, 43% of 3827 PLHIV practised inconsistent condom use at sexual intercourse with their regular partner. An even higher proportion, 46% of 2044 PLHIV admitted that they practised unprotected sex with a casual partner. Participants from Lao PDR reported the lowest prevalence of inconsistent condom use for both regular and casual partners, while participants from the Philippines had the highest risk behaviour. Inconsistent condom use was significantly associated with belonging to a key population (drug user, sex worker or refugee subpopulation), not knowing that condoms are still needed if both partners are HIV positive, having a regular partner whose HIV status was either positive or unknown, having experienced physical assault and not receiving antiretroviral treatment.ConclusionsThis large seven-country study highlights a high prevalence of inconsistent condom use among PLHIV in the Asia-Pacific region. In addition to knowledge-imparting interventions, the adoption and expansion of the ‘Test and Treat’ strategy could help to maximise the prevention benefits of antiretroviral treatment.
Complement Activation via a C3a Receptor Pathway Alters CD4+ T Lymphocytes and Mediates Lung Cancer Progression
Authors: Kwak Jeff W. , Laskowski Jennifer , Li Howard Y. , McSharry Maria V. , Sippel Trisha R. , Bullock Bonnie L. , Johnson Amber M. , Poczobutt Joanna M. , Neuwelt Alexander J. , Malkoski Stephen P. , Weiser-Evans Mary C. , Lambris John D. , Clambey Eric T. , Thurman Joshua M. , Nemenoff Raphael A. 
Published: November 2017

Abstract
The complement cascade is a part of the innate immune system that acts primarily to remove pathogens and injured cells. However, complement activation is also peculiarly associated with tumor progression. Here we report mechanistic insights into this association in multiple immunocompetent orthotopic models of lung cancer. After tumor engraftment, we observed systemic activation of the complement cascade as reflected by elevated levels of the key regulator C3a. Notably, growth of primary tumors and metastases was both strongly inhibited in C3-deficient mice (C3−/− mice), with tumors undetectable in many subjects. Growth inhibition was associated with increased numbers of IFNγ+/TNFα+/IL10+ CD4+ and CD8+ T cells. Immunodepletion of CD4+ but not CD8+ T cells in tumor-bearing subjects reversed the inhibitory effects of C3 deletion. Similarly, antagonists of the C3a or C5a receptors inhibited tumor growth. Investigations using multiple tumor cell lines in the orthotopic model suggested the involvement of a C3/C3 receptor autocrine signaling loop in regulating tumor growth. Overall, our findings offer functional evidence that complement activation serves as a critical immunomodulator in lung cancer progression, acting to drive immune escape via a C3/C5–dependent pathway.
Significance: This provocative study suggests that inhibiting complement activation may heighten immunotherapeutic responses in lung cancer, offering findings with immediate implications, given the existing clinical availability of complement antagonists. Cancer Res; 78(1); 143–56. ©2017 AACR.
Oncolytic Virotherapy Blockade by Microglia and Macrophages Requires STAT1/3
Authors: Delwar Zahid M. , Kuo Yvonne , Wen Yan H. , Rennie Paul S. , Jia William 
Published: November 2017

Abstract
The first oncolytic virotherapy employing HSV-1 (oHSV-1) was approved recently by the FDA to treat cancer, but further improvements in efficacy are needed to eradicate challenging refractory tumors, such as glioblastomas (GBM). Microglia/macrophages comprising approximately 40% of a GBM tumor may limit virotherapeutic efficacy. Here, we show these cells suppress oHSV-1 growth in gliomas by internalizing the virus through phagocytosis. Internalized virus remained capable of expressing reporter genes while viral replication was blocked. Macrophage/microglia formed a nonpermissive OV barrier, preventing dissemination of oHSV-1 in the glioma mass. The deficiency in viral replication in microglial cells was associated with silencing of particular viral genes. Phosphorylation of STAT1/3 was determined to be responsible for suppressing oHSV-1 replication in macrophages/microglia. Treatment with the oxindole/imidazole derivative C16 rescued oHSV-1 replication in microglia/macrophages by inhibiting STAT1/3 activity. In the U87 xenograft model of GBM, C16 treatment overcame the microglia/macrophage barrier, thereby facilitating tumor regression without causing a spread of the virus to normal organs. Collectively, our results suggest a strategy to relieve a STAT1/3-dependent therapeutic barrier and enhance oHSV-1 oncolytic activity in GBM.
Significance: These findings suggest a strategy to enhance the therapeutic efficacy of oncolytic virotherapy in glioblastoma. Cancer Res; 78(3); 718–30. ©2017 AACR.
Muscadine Grape Skin Extract (MPX) in Men with Biochemically Recurrent Prostate Cancer: A Randomized, Multicenter, Placebo-Controlled Clinical Trial
Authors: Paller Channing J. , Zhou Xian C. , Heath Elisabeth I. , Taplin Mary-Ellen , Mayer Tina , Stein Mark N. , Bubley Glenn J. , Pili Roberto , Hudson Tamaro , Kakarla Radhika , Abbas Muneer M. , Anders Nicole M. , Dowling Donna , King Serina , Bruns Ashley B. , Wagner William D. , Drake Charles G. , Antonarakis Emmanuel S. , Eisenberger Mario A. , Denmeade Samuel R. , Rudek Michelle A. , Rosner Gary L. , Carducci Michael A. 
Published: November 2017

Abstract
Purpose: MuscadinePlus (MPX), a commercial preparation of pulverized muscadine grape skin, was evaluated as a therapeutic option for men with biochemically recurrent (BCR) prostate cancer wishing to defer androgen deprivation therapy.
Experimental Design: This was a 12-month, multicenter, placebo-controlled, two-dose, double-blinded trial of MPX in 125 men with BCR prostate cancer, powered to detect a PSA doubling time (PSADT) difference of 6 months (low dose) and 12 months (high dose) relative to placebo. Participants were stratified (baseline PSADT, Gleason score) and randomly assigned 1:2:2 to receive placebo, 500 mg MPX (low), or 4,000 mg MPX (high) daily. Correlates included superoxide dismutase-2 (SOD2) genotype, lipid peroxidation, and polyphenol pharmacokinetics.
Results: The evaluable population included 112 patients, all treated for at least 6 months and 62% treated for 12 months. No significant difference was found in PSADT change between control and treatment arms (P = 0.81): control 0.9 months (n = 20; range, 6.7–83.1), low dose 1.5 months (n = 52; range, 10.3–87.2), high dose 0.9 months (n = 40; range, 27.3–88.1). One high-dose patient experienced objective response. No drug-related CTCAE grade 3–4 adverse events were seen. In a preplanned exploratory analysis, PSADT pre-to-post increase was significant in the 27 (26%) genotyped patients with SOD2 Alanine/Alanine genotype (rs4880 T&gt;C polymorphism) on MPX (pooled treatment arms; 6.4 months, P = 0.02), but not in control (1.8 months, P = 0.25).
Conclusions: Compared with placebo, MPX did not significantly prolong PSADT in BCR patients over two different doses. Exploratory analysis revealed a patient population with potential benefit that would require further study. Clin Cancer Res; 24(2); 306–15. ©2017 AACR.
Chemoprevention with Cyclooxygenase and Epidermal Growth Factor Receptor Inhibitors in Familial Adenomatous Polyposis Patients: mRNA Signatures of Duodenal Neoplasia
Authors: Delker Don A. , Wood Austin C. , Snow Angela K. , Samadder N. Jewel , Samowitz Wade S. , Affolter Kajsa E. , Boucher Kenneth M. , Pappas Lisa M. , Stijleman Inge J. , Kanth Priyanka , Byrne Kathryn R. , Burt Randall W. , Bernard Philip S. , Neklason Deborah W. 
Published: November 2017

AbstractTo identify gene expression biomarkers and pathways targeted by sulindac and erlotinib given in a chemoprevention trial with a significant decrease in duodenal polyp burden at 6 months (P &lt; 0.001) in familial adenomatous polyposis (FAP) patients, we biopsied normal and polyp duodenal tissues from patients on drug versus placebo and analyzed the RNA expression. RNA sequencing was performed on biopsies from the duodenum of FAP patients obtained at baseline and 6-month endpoint endoscopy. Ten FAP patients on placebo and 10 on sulindac and erlotinib were selected for analysis. Purity of biopsied polyp tissue was calculated from RNA expression data. RNAs differentially expressed between endpoint polyp and paired baseline normal were determined for each group and mapped to biological pathways. Key genes in candidate pathways were further validated by quantitative RT-PCR. RNA expression analyses of endpoint polyp compared with paired baseline normal for patients on placebo and drug show that pathways activated in polyp growth and proliferation are blocked by this drug combination. Directly comparing polyp gene expression between patients on drug and placebo also identified innate immune response genes (IL12 and IFNγ) preferentially expressed in patients on drug. Gene expression analyses from tissue obtained at endpoint of the trial demonstrated inhibition of the cancer pathways COX2/PGE2, EGFR, and WNT. These findings provide molecular evidence that the drug combination of sulindac and erlotinib reached the intended tissue and was on target for the predicted pathways. Furthermore, activation of innate immune pathways from patients on drug may have contributed to polyp regression. Cancer Prev Res; 11(1); 4–15. ©2017 AACR.See related editorial by Shureiqi, p. 1
The Yogācārabhūmi against Allodoxies (paravāda): 2 Ritual Violence
Authors: Eltschinger Vincent 
Published: November 2017

The Yogācārabhūmi, a massive compilation of the early Yogācāra “school(s),” contains a comparatively short section dedicated to the critical examination of sixteen “allodoxies” (paravāda), mostly non-Buddhist doctrines, practices and institutions, some of which go back to the Brahmajāla- and Śrāmaṇyaphalasūtra of the Dīrghāgama. This section, which could be dated to the late 3rd century CE, is a remarkable milestone in the history of philosophy in the Buddhist environment, in that it summarizes and updates earlier, canonical arguments, adapting them to a new polemical context, and reveals Buddhist philosophy’s profound indebtedness to sūtra literature. The present paper analyzes allodoxy no. 8 (hiṃsādharmavāda), the brahmins’ claim that ritual violence is a religious duty and, as such, no violence at all. The Yogācārabhūmi’s arguments are among the most cogent and systematic Indian Buddhists ever directed against ritual violence.
A Statistical Study of Unusual Tracks of Tropical Cyclones near Taiwan Island
Authors: Gong Yueting , Li Ying , Zhang Da-Lin 
Published: November 2017

AbstractTropical cyclones (TCs) tend to change translation direction and speed when moving across Taiwan’s Central Mountain Range (CMR), which makes forecasting of landfalling points a challenging task. This study examines the statistical characteristics of unusual TC tracks around Taiwan Island during the 66-yr period of 1949–2014. Results show that 1) about 10% more TCs were deflected to the right than to the left as they moved across the CMR, but with more occurrences of the latter on Taiwan’s eastern coast and southern strait; 2) TCs around Taiwan Island moved slower than the average speed over the western North Pacific Ocean but then exhibited anomalous acceleration along Taiwan’s eastern coast and anomalous deceleration over the southern Taiwan Strait; 3) about 33% of TCs passing the island were accompanied by terrain-induced secondary low pressure centers (SCs), more favored in the northwestern, southwestern, and southeastern quadrants, with the TC–SC separation distance varying from 33 to 643 km; 4) about 36% of landfalling TCs experienced discontinuous tracks, with an average separation distance of 141 km at the time when TC centers were replaced by SCs, and smaller Froude numbers than those associated with continuous-tracking TCs; and 5) a total of 12 TCs had looping movements near Taiwan Island, most of which were accompanied by SCs on their southern or western sides. Results also indicate that a stronger SC was likely to take place when a stronger TC approached the CMR with a shorter separation distance and that a weaker SC was likely to take place when a weaker TC approached the CMR with a longer separation distance.
ENSO Effects on Annual Variations of Summer Precipitation Stable Isotopes in Lhasa, Southern Tibetan Plateau
Authors: Gao Jing , He You , Masson-Delmotte Valerie , Yao Tandong 
Published: November 2017

Abstract
Although El Niño–Southern Oscillation (ENSO) influences the Indian summer monsoon, its impact on moisture transport toward the southern Tibetan Plateau (TP) remains poorly understood. Precipitation stable isotopes are useful indices for climate change in the TP. Classical interpretations of variations of precipitation stable isotopes focus on the local surface air temperature or precipitation amount. However, several of the latest studies suggested they may correlate with large-scale modes of variability, such as ENSO. This paper presents a detailed study of ENSO’s effect on annual variations of the oxygen stable isotopic composition of precipitation (δ18Op) at Lhasa in the southern TP for up to 10 years. The stable isotopic composition of water vapor from satellite data [Tropospheric Emission Spectrometer (TES)] and simulations from an isotopically enabled atmospheric general circulation model (zoomed LMDZiso) are used to explore the mechanism that leads to variations of δ18Op at Lhasa. Statistically significant correlations between δ18Op and ENSO indices [Southern Oscillation index (SOI) and Niño-3.4 sea surface temperature index (Niño-3.4)] are observed. This paper shows that ENSO’s effects on the location and intensity of convection over the Arabian Sea, the Bay of Bengal, and the tropical Indian Ocean, along moisture transport paths toward Lhasa, further impact convection from the northern Tibetan Plateau. The changing of this convection results in lower δ18Op at Lhasa in 2007, a La Niña year, and higher δ18Op in 2006, an El Niño year. The study presented here confirms that the regional upstream convection related to ENSO teleconnections plays an important role in variations of δ18Op at the interannual scale and that the more depleted oxygen stable isotopic composition of vapor (δ18Oυ) from the northwestern region of India during a La Niña year intensifies the lower δ18Op at Lhasa in a La Niña year. The study’s results have implications for the interpretation of past variations of archives with precipitation stable isotopes, such as ice cores, tree rings, lake sediments, and speleothems, in this region.