Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.

In the version of this article initially published online, two pairs of headings were switched with each other in Table 4: "Recall (PCR free)" was switched with "Recall (with PCR)," and "Precision (PCR free)" was switched with "Precision (with PCR)." The error has been corrected in the print, PDF and HTML versions of this article.

Best practices for benchmarking germline small-variant calls in human genomes.

Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling.

Long-term overall- and progression-free survival after pentostatin, cyclophosphamide and rituximab therapy for indolent non-Hodgkin lymphoma.

In a prospective phase II trial, pentostatin combined with cyclophosphamide and rituximab (PCR) induced strong responses and was well-tolerated in previously untreated patients with advanced-stage, indolent non-Hodgkin lymphoma (iNHL). After a median patient follow-up of more than 108 months, we performed an intent-to-treat analysis of our 83 participants. Progression-free survival (PFS) rates at 108 months for follicular lymphoma (FL), marginal zone lymphoma (MZL) and small lymphocytic lymphoma (SLL) were 71%, 67% and 15%, respectively, and were affected by clinicopathological characteristics.

Comparison of visual and optical quality of monofocal versus multifocal intraocular lenses.

Objective: To compare visual quality in patients implanted with Tecnis monofocal (ZCB00) and multifocal (ZMB00) intraocular lenses taking into account their optical quality measured in vitro with an eye model.

Methods: In total, 122 patients participated in this study: 44 implanted with monofocal and 78 with multifocal intraocular lenses. Measurements of visual acuity and contrast sensitivity were performed.

Ability of Cytisus scoparius for phytoremediation of soils from a Pb/Zn mine: Assessment of metal bioavailability and bioaccumulation.

Abandoned mining areas are an environmental concern for aquatic and terrestrial ecosystems due to their unfavourable soil properties and high levels of potentially toxic elements. Despite this, some plant species may grow spontaneously and colonise these areas; being suitable in many cases for restoration practices, since they may accumulate metals in their tissues. This study aims to assess the effectiveness of 14 chemical soil extractants to predict the bioavailability of toxic elements (Cd, Pb and Zn) in soils from the abandoned Pb/Zn mine of Rubiais (NW Spain), based on root and shoot metal contents in Cytisus scoparius (L.

Emergence of chikungunya and Zika in a municipality endemic to dengue, Santa Luzia, MG, Brazil, 2015-2017.

Introduction: The recent circulation of arboviruses transmitted by vectors, such as dengue, chikungunya, and Zika, is concerning due to the high morbidity rates, clinical complications, and increased demand on health services. The objective of this study was to analyze the clinical and epidemiological aspects of an epidemic caused by arboviruses in the municipality of Santa Luzia, Minas Gerais, Brazil.

Methods: Longitudinal study of patients with acute febrile disease and suspected arbovirus infection reported to Brazilian Notifiable Disease Information System (Sistema de Informação de Agravos de Notificação) from the epidemiological week 44 of 2015 to epidemiological week 52 of 2016.

Polygenic risk scores: a biased prediction?

A new study highlights the biases and inaccuracies of polygenic risk scores (PRS) when predicting disease risk in individuals from populations other than those used in their derivation. The design bias of workhorse tools used for research, particularly genotyping arrays, contributes to these distortions. To avoid further inequities in health outcomes, the inclusion of diverse populations in research, unbiased genotyping, and methods of bias reduction in PRS are critical.

Organoid Modeling of the Tumor Immune Microenvironment.

In vitro cancer cultures, including three-dimensional organoids, typically contain exclusively neoplastic epithelium but require artificial reconstitution to recapitulate the tumor microenvironment (TME). The co-culture of primary tumor epithelia with endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has been particularly elusive. Here, an air-liquid interface (ALI) method propagated patient-derived organoids (PDOs) from >100 human biopsies or mouse tumors in syngeneic immunocompetent hosts as tumor epithelia with native embedded immune cells (T, B, NK, macrophages).

Observing the devastating coffee berry borer (Hypothenemus hampei) inside the coffee berry using micro-computed tomography.

The coffee berry borer is the most devastating insect pest of coffee throughout the world. The insect spends most of its life cycle inside the coffee berry, which makes it quite difficult to observe its behaviour. Micro-computed tomography (micro-CT) was used to observe all developmental stages of the coffee berry borer inside coffee berries (Coffea canephora).

A mid-Cretaceous ambrosia fungus, Paleoambrosia entomophila gen. nov. et sp. nov. (Ascomycota: Ophiostomatales) in Burmese (Myanmar) amber, and evidence for a femoral mycangium.

An ambrosia fungus is described from filamentous sporodochia adjacent to a wood-boring ambrosia beetle (Coleoptera: Curculionidae: Platypodinae) in mid-Cretaceous Burmese amber. Yeast-like propagules and hyphal fragments of Paleoambrosia entomophila gen. nov.

Selective Laser Sintering of Laser Printed Ag Nanoparticle Micropatterns at High Repetition Rates.

The increasing development of flexible and printed electronics has fueled substantial advancements in selective laser sintering, which has been attracting interest over the past decade. Laser sintering of metal nanoparticle dispersions in particular (from low viscous inks to high viscous pastes) offers significant advantages with respect to more conventional thermal sintering or curing techniques. Apart from the obvious lateral selectivity, the use of short-pulsed and high repetition rate lasers minimizes the heat affected zone and offers unparalleled control over a digital process, enabling the processing of stacked and pre-structured layers on very sensitive polymeric substrates.

Visual acuity of pseudophakic patients predicted from measurements of intraocular lenses with different design.

The optical quality of a set of IOLs (modeling set: one monofocal and two bifocals) was assessed through focus by the area under the modulation transfer function (MTFa) metric and related to the visual acuity (VA) defocus curves of pseudophakic patients implanted with said IOLs. A non-linear relationship between the MTFa and clinical VA was obtained with an asymptotic limit found to be the best VA achievable by the patients. Two mathematical fitting functions between clinical VA and MTFa were derived with high correlation coefficients (R≥0.

Smoothened stabilizes and protects TRAF6 from degradation: A novel non-canonical role of smoothened with implications in lymphoma biology.

Tumor necrosis factor receptor-associated factor 6 (TRAF6), an (K63) E3-ligase, plays a role in many biological processes and its activity is relevant in diffuse large B cell lymphoma (DLBCL) biology. Although molecules that trigger TRAF6 activation have been defined, those that stabilize TRAF6 and/or enhance TRAF6 function remain largely unclear. We found that TRAF6 amplifies pAKT signaling in DLBCL.

Micro-CT to Document the Coffee Bean Weevil, (Coleoptera: Anthribidae), Inside Field-Collected Coffee Berries ().

The coffee bean weevil, (De Geer) (Coleoptera: Anthribidae), is a cosmopolitan insect with >100 hosts, and has been reported as a pest of stored coffee. During a study involving the coffee berry borer, we observed coffee bean weevils emerging from field-collected coffee berries and used micro-computerized tomography (micro-CT) scans to observe the insect inside the berry. Two eggs had eclosed inside the berry, resulting in observations of a newly eclosed adult beetle and a 5th instar larva, each feeding on one of the two seeds.