bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperate Phages of
Staphylococcus aureus
Authors: Ingmer Hanne , Gerlach David , Wolz Christiane 
Published: September 2019

ABSTRACT

Most
Staphylococcus aureus
isolates carry multiple bacteriophages in their genome, which provide the pathogen with traits important for niche adaptation. Such temperate
S. aureus
phages often encode a variety of accessory factors that influence virulence, immune evasion and host preference of the bacterial lysogen. Moreover, transducing phages are primary vehicles for horizontal gene transfer. Wall teichoic acid (WTA) acts as a common phage receptor for staphylococcal phages and structural variations of WTA govern phage-host specificity thereby shaping gene transfer across clonal lineages and even species. Thus, bacteriophages are central for the success of
S. aureus
as a human pathogen.
The glacial record in regions surrounding the Driftless Area
Authors: Carson* Eric C. , Attig John W. , Rawling III J. Elmo 
Published: September 2019

ABSTRACT
The Driftless Area of southwestern Wisconsin is defined by its lack of glacial deposits; therefore, the geographic limits of the Driftless Area are delimited by glacial deposits of various ages. The northern boundary of the Driftless Area is marked by the patchy distribution of pre-Illinoian (pre–marine oxygen isotope stage [MIS] 8) deposits that contain clasts from the north and northwest. The western margin is also delimited by pre–MIS 8 sediments that extend roughly coincident with the Mississippi River. This boundary is best identified by the topographic feature of the Bridgeport moraine near the confluence of the Mississippi and Wisconsin rivers and by the presence of patchy till underlying MIS 2 loess on upland surfaces in southwesternmost Wisconsin. The southeastern margin is delimited by extensive Illinoian (MIS 6–8) deposits with eroded glacial landforms evident in modern light detection and ranging (LiDAR)–derived digital elevation models. The eastern margin is marked by well-preserved glacial landforms and sediment associated with the MIS 2 glaciation. The Green Bay Lobe of the Laurentide Ice Sheet deposited prominent moraines that dammed numerous ice-proximal lakes. The most significant of these was glacial Lake Wisconsin, which formed when the Green Bay Lobe dammed the Wisconsin River at the east end of the Baraboo Hills. The most recent episode of permafrost in the Driftless Area lasted from ca. 33 to 14 ka; a suite of permafrost-related features that formed sometime during this time period can be found throughout the Driftless Area.
Loess, eolian sand, and colluvium in the Driftless Area
Authors: Mason* Joseph A. , Jacobs Peter M. , Leigh David S. 
Published: September 2019

ABSTRACT
Loess mantles upland summits across much of the Driftless Area of southwestern Wisconsin and its origin and paleoenvironmental significance has been a focus of research since the nineteenth century. Although the Driftless Area was ice free through the many glaciations of the Quaternary, long-term preservation of loess was limited by post-depositional erosion across much if not all of this highly dissected landscape, erosion that was likely accelerated under periglacial conditions during glaciations when ice sheets were nearby. Loess preserved today includes four members of the Kieler Formation and two older loesses known only from one locality. The Peoria Member, the youngest, thickest, and most extensive member of the Kieler Formation, was deposited during and just after the peak of the last glaciation. Its main sources include both the Mississippi River valley and the Iowan Erosion Surface and glacial outwash surfaces farther west in Iowa and Minnesota. More research is needed on the relative contribution from each of these sources to the Peoria Member, and on the sources of older loess units. Eolian sand, often forming dunes, covers extensive low-relief landscapes in the northern Driftless Area, the Mississippi and Wisconsin River valleys, and smaller areas elsewhere in the region, overlying sandstone bedrock, stream terraces, and the former bed of Glacial Lake Wisconsin. These sands are stabilized by vegetation today but were active during and just after the period of Peoria Member deposition. Thus, large areas of eolian sand acted as surfaces of transport where loess did not accumulate but rather was conveyed far downwind of its sources. Colluvium that is a mixture of bedrock-derived sediment and loess covers bedrock slopes throughout the Driftless Area. A variety of geochronologic, geomorphic, and stratigraphic evidence supports the hypothesis that this colluvial mantle formed mainly in the cold, periglacial environment of the last glaciation, with only limited modification during the Holocene. A new research effort, incorporating modern geochemical and geochronological techniques, could provide important insights on the processes that originally produced the colluvial mantle and those that are acting on it today.
Holocene paleohydrology and paleofloods in the Driftless Area
Authors: Daniels* J. Michael , Leigh David S. , Carson Eric C. 
Published: September 2019

ABSTRACT
The study of Holocene paleohydrology and paleofloods represents one of James C. Knox’s most enduring contributions to our understanding of the geology and physical geography of the Driftless Area. His work on these subjects resulted in over 20 journal articles, refereed book chapters, field-trip guidebooks, and unpublished reports over a period of 40 years. By systematically amassing a wealth of radiocarbon-dated morphologic, stratigraphic, and sedimentologic observations, he was able to quantitatively document changing hydrologic conditions in the region over the past 11.7 ka. He extended these empirical results to establish a broadly applicable theoretical perspective about the profound hydrologic and geomorphologic impacts of even modest changes in climate. This theory, grounded in field-derived data collection, detailed sedimentological analysis, statistical methods, and contextual analysis of supplementary paleoenvironmental evidence, has important implications for our understanding of changing flood magnitudes and frequencies in response to ongoing climate change. Knox pioneered novel methods for reconstructing past hydrologic variability. His work on the cross-sectional geometry of paleomeanders provides a direct proxy for estimation of high-frequency, low-magnitude bankfull floods. His analysis of overbank gravels facilitates reconstruction of an early through late Holocene time-series of large, infrequent floods. His attention to sandy beds occurring within uninterrupted, fine-grained, overbank depositional sequences enables continuous magnitude and frequency analysis of floods to be extended hundreds, even thousands, of years beyond the modern gaging record. We demonstrate this with statistical correlation of a gaging record to &gt;0.25 mm sand contents at one of Knox’s former sites. By quantifying hydrologic change in the Driftless Area over millennial timescales, Knox’s work demonstrates conclusively the non-stationarity of flood magnitudes and frequencies, a result that has significance for fluvial geomorphology, paleohydrology, water resource management, and flood mitigation. The scientific and societal value of these results continues to increase in relevance for the future.
Quality of investigations into unexpected deaths of infants and young children in England after implementation of national child death review procedures in 2008: a retrospective assessment
Authors: Fleming Peter , Pease Anna , Ingram Jenny , Sidebotham Peter , Cohen Marta C , Coombs Robert C , Ewer Andrew K , Ward Platt Martin , Fox John , Marshall David , Lewis Anne , Evason-Coombe Carol , Blair Peter 
Published: September 2019

ObjectivesIn 2008, new statutory national procedures for responding to unexpected child deaths were introduced throughout England. There has, to date, been no national audit of these procedures.Study designFamilies bereaved by the unexpected death of a child under 4 years of age since 2008 were invited to participate. Factors contributing to the death and investigations after the death were explored. Telephone interviews were conducted, and coroners’ documents were obtained. The nature and quality of investigations was compared with the required procedures; information on each case was reviewed by a multiagency panel; and the death was categorised using the Avon clinicopathological classification.ResultsData were obtained from 91 bereaved families (64 infant deaths and 27 children aged 1–3 years); 85 remained unexplained after postmortem examination. Documentation of multiagency assessments was poorly recorded. Most (88%) families received a home visit from the police, but few (37%) received joint visits by police and healthcare professionals. Postmortem examinations closely followed national guidance; 94% involved paediatric pathologists; 61% of families had a final meeting with a paediatrician to explain the investigation outcome. There was no improvement in frequency of home visits by health professionals or final meetings with paediatricians between 2008–2013 and 2014–2017 and no improvement in parental satisfaction with the process.ConclusionsStatutory procedures need to be followed more closely. The implementation of a national child mortality database from 2019 will allow continuing audit of the quality of investigations after unexpected child deaths. An important area amenable to improvement is increased involvement by paediatricians.
Identifying central serous chorioretinopathy biomarkers in coexisting diabetic retinopathy: a multimodal imaging study
Authors: Dhurandhar Deven Sushil , Singh Sumit Randhir , Sahoo Niroj Kumar , Goud Abhilash , Lupidi Marco , Chhablani Jay 
Published: September 2019

BackgroundTo describe clinical and imaging characteristics of patients presenting with diabetic retinopathy (DR) with coexisting acute or chronic central serous chorioretinopathy (CSCR).MethodsThis was a cross-sectional study which included 54 eyes of 27 patients with coexisting DR and CSCR. Demographic details, prior history of laser, best-corrected visual acuity (BCVA), central macular thickness (CMT), height of neurosensory detachment (NSD), subfoveal choroidal thickness (SFCT), subfoveal large choroidal vessel layer thickness (SF-LCVT), fluorescein angiography and indocyanine green angiography features were recorded. Subanalysis was done for patients with unilateral CSCR. Data was evaluated using Student t-test for quantitative data and χ2 test for qualitative data. CSCR between different grades of DR was analysed using analysis of variance.ResultsPrevalence of coexistent CSCR in eyes with DR was 0.4%. Mean age was 53.96±8.79 years, with 25 males. Mean CMT was 349.2±258 μm. Mean SFCT and SF- LCVT of 38 eyes were 376.40±86 μm and 178.80±62.8 μm, respectively. Fifteen eyes had centre involving diabetic macular oedema. Subanalysis of patients with unilateral CSCR showed that the loss of inner segment-outer segment (IS-OS) integrity (p=0.001), photoreceptor footplates at the NSD roof (p=0.001) on optical coherence tomography and dilated choroidal vessels (p=0.05) on indocyanine green angiography were found more often in the CSCR eyes compared with their fellow eyes. Features of CSCR among the different grades of DR were not significantly different between the groups.ConclusionOur study describes features of a unique subset of patients presenting with coexistent DR and CSCR. Such coexistent nature needs special attention by the clinicians as this may change the treatment approach and alter outcomes.
Classifying juvenile onset primary open angle glaucoma using cluster analysis
Authors: Birla Shweta , Gupta Dinesh , Somarajan Bindu I , Gupta Shikha , Chaurasia Abadh Kishore , Kishan Azmira , Gupta Viney 
Published: September 2019

AimTo classify unrelated patients with juvenile onset primary open angle glaucoma (JOAG) into clinically useful phenotypes using cluster analysis.MethodsOut of the 527 unrelated patients with JOAG, the study included 414 patients who had all the phenotypic characteristics required for the study. A cluster analysis was performed to classify the patients based on their iris and angle morphology, age of onset, highest untreated intraocular pressure (IOP), worst mean deviation and greatest vertical cup disc ratio of the worst eye. The iris features were broadly classified into three groups: those with normal iris crypts (NIC), those with prominent iris crypts (PIC) and those with absence of iris crypts. The gonio photographs were graded as normal appearing angle or those with angle dysgenesis in the form of a featureless angle, one with a high iris insertion and an angle with prominent iris processes. Using a hierarchical clustering model and a two-way cluster analysis, the distribution of clusters of JOAG was analysed to obtain a classification of JOAG subtypes.ResultsThe four major clusters identified were: Cluster 1 with NIC and normal angles had the lowest untreated IOP and higher age of onset among all clusters. Cluster 2 with NIC and featureless angle was found to be associated with earliest age of onset. Cluster 3 had NIC and either a high iris insertion or prominent iris processes. Cluster 4 was a heterogeneous cluster with maximum number of patients in a group comprising of those with PIC and high iris insertion.ConclusionsCluster analysis extracted four subgroups of the JOAG phenotype that have clinical and prognostic significance and can potentially be helpful while evaluating these patients in the clinics.
Effect of posterior vitreous detachment on treat-and-extend versus monthly ranibizumab for neovascular age-related macular degeneration
Authors: Waldstein Sebastian M , Coulibaly Leonard , Riedl Sophie , Sadeghipour Amir , Gerendas Bianca S , Schmidt-Erfurth Ursula Margarethe 
Published: September 2019

AimsTo investigate the impact of posterior vitreous detachment (PVD) on the efficacy of treat-and-extend (T&E) ranibizumab in neovascular age-related macular degeneration.MethodsIn a post hoc analysis of a randomised controlled clinical trial, spectral-domain optical coherence tomography images of treatment-naïve patients randomised to receive T&E (n=265) or monthly (n=264) ranibizumab for 12 months were included. Certified, masked graders diagnosed the presence or the absence of complete PVD. The main outcome measures were the mean change in best-corrected visual acuity (BCVA) and central retinal thickness (CRT) at month 12, the number of administered ranibizumab injections and the proportion of patients extended to more than 8 weeks.ResultsAt baseline, complete PVD was present in 51% and 56% of patients in the monthly and T&E arms, respectively. Mean change in BCVA at month 12 was +9.0 (PVD) vs +9.5 letters (no PVD, p=0.78) in monthly treated eyes, and +6.0 (PVD) vs +7.5 letters (no PVD, p=0.42) in T&E treated eyes. Conversely, mean change in CRT at month 12 was −174 (PVD) vs −173 µm (no PVD, p=0.98) in the monthly arm, and −175 (PVD) vs −164 µm (no PVD, p=0.58) in the T&E arm. In T&E treated patients, the median number of injections was eight vs nine (p=0.035). 71% of PVD eyes were extended successfully, compared with 55% of eyes without PVD (p=0.005).ConclusionPVD was not found to impact functional and anatomical outcomes of T&E ranibizumab therapy. However, patients without a complete PVD required more retreatments and were significantly less likely to be successfully extended.Trial registration numberNCT01948830
Adverse events of exercise therapy in randomised controlled trials: a systematic review and meta-analysis
Authors: Niemeijer Andre , Lund Hans , Stafne Signe Nilssen , Ipsen Thomas , Goldschmidt Cathrine Luhaäär , Jørgensen Claus Thomas , Juhl Carsten B 
Published: September 2019

ObjectiveTo evaluate the relative risk (RR) of serious and non-serious adverse events in patients treated with exercise therapy compared with those in a non-exercising control group.DesignSystematic review and meta-analysis.Data sourcesPrimary studies were identified based on The Cochrane Database of Systematic Reviews investigating the effect of exercise therapy.Eligibility criteriaAt least two of the authors independently evaluated all identified reviews and primary studies. Randomised controlled trials were included if they compared any exercise therapy intervention with a non-exercising control. Two authors independently extracted data. The RR of serious and non-serious adverse events was estimated separately.Results180 Cochrane reviews were included and from these, 773 primary studies were identified. Of these, 378 studies (n=38 368 participants) reported serious adverse events and 375 studies (n=38 517 participants) reported non-serious adverse events. We found no increase in risk of serious adverse events (RR=0.96 (95%CI 0.90 to 1.02, I2: 0.0%) due to exercise therapy. There was, however, an increase in non-serious adverse events (RR=1.19 (95%CI 1.09 to 1.30, I2: 0.0%). The number needed to treat for an additional harmful outcome for non-serious adverse events was 6 [95%CI 4 to 11).ConclusionParticipating in an exercise intervention increased the relative risk of non-serious adverse events, but not of serious adverse events. Exercise therapy may therefore be recommended as a relatively safe intervention.PROSPERO registration numberCRD42014014819.
Subclinical ochronosis features in alkaptonuria: a cross-sectional study
Authors: Cox Trevor , Psarelli Eftychia Eirini , Taylor Sophie , Shepherd Hannah Rose , Robinson Mark , Barton Gabor , Mistry Alpesh , Genovese Federica , Braconi Daniela , Giustarini Daniela , Rossi Ranieri , Santucci Annalisa , Khedr Milad , Hughes Andrew , Milan Anna , Taylor Leah Frances , West Elizabeth , Sireau Nicolas , Dillon Jane Patricia , Rhodes Nicholas , Gallagher James Anthony , Ranganath Lakshminarayan 
Published: September 2019

BackgroundAlkaptonuria (AKU) is present from birth, yet clinical effects are considered to appear later in life. Morbidity of AKU, considered irreversible, is secondary to ochronosis. Age of ochronosis onset is not clearly known. Nitisinone profoundly lowers homogentisic acid (HGA), the metabolic defect in AKU. Nitisinone also arrests ochronosis and slows progression of AKU. However, tyrosinaemia post-nitisinone has been associated with corneal keratopathy, rash and cognitive impairment in HT 1. The optimal time to start nitisinone in AKU is unknown.MethodsIn an open, cross-sectional, single-site study, 32 patients with AKU were to be recruited. The primary outcome was presence of ochronosis in an ear biopsy. Secondary outcomes included analysis of photographs of eyes/ears, serum/urine HGA, markers of tissue damage/inflammation/oxidation, MRI imaging, gait, quality of life and Alkaptonuria Severity Score Index (qAKUSSI).ResultsThirty patients, with mean age (SD) 38 (14) years, were recruited. Percentage pigmentation within ear biopsies increased with age. Ear pigmentation was detected in a 20-year-old woman implying ochronosis can start in patients before the age of 20. Gait and qAKUSSI were outside the normal range in all the patients with AKU.ConclusionsOchronosis can be present before age 20 years.
Age, cancer site and gender associations with symptoms and problems in specialised palliative care: a large, nationwide, register-based study
Authors: Hansen Maiken Bang , Ross Lone , Petersen Morten Aagaard , Groenvold Mogens 
Published: September 2019

BackgroundPatients referred to specialised palliative care are troubled by symptoms/problems, but more knowledge is needed on the level and frequency of symptoms/problems. It is also uncertain how gender, age and cancer diagnosis, respectively, are associated with symptoms/problems.AimsTo describe symptoms/problems in patients with cancer at the start of specialised palliative care, and to study how age, gender and cancer diagnosis were associated with symptoms/problems.DesignA register-based study including data from the Danish Palliative Care Database.Setting/ParticipantsPatients with cancer who reported their symptoms/problems using the European Organisation for Research and Treatment of Cancer Quality of Life Questionaire-Core-15-Palliative Care (EORTC QLQ-C15-PAL) at the start of specialised palliative care were included. Ordinal logistic regression was performed to test if gender, age and cancer diagnosis were associated with each symptom/problem.Results31 771 patients with cancer were included in the study. The most prevalent and severe symptoms/problems were pain, appetite loss, fatigue, poor physical function and poor quality of life. Gender, age and cancer diagnosis were significantly associated with most symptoms/problems. The strongest associations between symptoms/problems and gender and age, respectively, were increased risk of nausea in women, as well as increased risk of poor physical function and reduced risk of sleeplessness and pain with increasing age. Patients with brain/central nervous system cancer had the lowest risk of symptoms but the highest risk of poor physical function.ConclusionAt the start of specialised palliative care, patients with cancer experience severe levels of symptoms, poor physical function and poor quality of life. Age, gender and diagnosis were significantly associated with most symptoms/problems, but the strength and direction of the associations differed across symptoms/problems.
How to perform a meta-analysis with R: a practical tutorial
Authors: Balduzzi Sara , Rücker Gerta , Schwarzer Guido 
Published: September 2019

ObjectiveMeta-analysis is of fundamental importance to obtain an unbiased assessment of the available evidence. In general, the use of meta-analysis has been increasing over the last three decades with mental health as a major research topic. It is then essential to well understand its methodology and interpret its results. In this publication, we describe how to perform a meta-analysis with the freely available statistical software environment R, using a working example taken from the field of mental health.MethodsR package meta is used to conduct standard meta-analysis. Sensitivity analyses for missing binary outcome data and potential selection bias are conducted with R package metasens. All essential R commands are provided and clearly described to conduct and report analyses.ResultsThe working example considers a binary outcome: we show how to conduct a fixed effect and random effects meta-analysis and subgroup analysis, produce a forest and funnel plot and to test and adjust for funnel plot asymmetry. All these steps work similar for other outcome types.ConclusionsR represents a powerful and flexible tool to conduct meta-analyses. This publication gives a brief glimpse into the topic and provides directions to more advanced meta-analysis methods available in R.