bluuebunny/crossref_metadata_2025 huggingface dataset:
Terahertz near-field microscopy of ductal carcinoma in situ (DCIS) of the breast
Authors: Okada Kosuke , Serita Kazunori , Cassar Quentin , Murakami Hironaru , MacGrogan Gaëtan , Guillet Jean-Paul , Mounaix Patrick , Tonouchi Masayoshi
Published: October 2020

Imaging with terahertz (THz) waves has been expected as a non-invasive/non-staining visualization tool for breast cancer margins during surgeries. Breast cancer is a generic name for a heterogeneous lesion comprising invasive adenocarcinoma, in situ adenocarcinoma, most frequently in the form of ductal carcinoma in situ (DCIS) and benign tissues. Until now, THz imaging has focused on invasive adenocarcinoma; however, THz analysis of DCIS has hardly been performed. One of the reasons is that the size of an individual DCIS lesion, ranging from 50 to 500 µm, is typically much smaller than that of an invasive carcinoma. This makes it difficult to identify these lesions by THz imaging, which has only a diffraction-limited spatial resolution of several millimeters. To overcome this drawback, we have developed a scanning point terahertz source (SPoTS) microscope with a resolution of 20 µm, in which a near-infrared-pump-laser-induced two-dimensionally-scannable point THz source (φ
THz ≈ φ
Pump) generated in a GaAs crystal contacts a sample. In this study, utilizing this state-of-the-art microscope, we mainly performed THz near-field transmission imaging of a paraffin-embedded human breast cancer sample containing invasive carcinoma and DCIS, as a preliminary study. Consequently, for the first time, we succeeded in clearly visualizing a DCIS lesion of ∼φ500 µm in the THz images. It was also found that the THz attenuation by DCIS was higher than that by invasive ductal carcinoma. Furthermore, also in a reflection-mode measurement, we successfully obtained a similar outcome to the above transmission-mode one. These results can be caused by the interaction between the THz waves and the cellular density, indicating that SPoTS microscopy may be suitable for DCIS diagnosis.
6. Conquests
Authors: Restall Matthew , Solari Amara
Published: October 2020

“Conquests” gives a history of the Spanish invasions of late Postclassic Maya states in the sixteenth century. Whether these invasions could be called conquests at all is debatable. These incursions were protracted and incomplete. The fragmentary, plural nature of Maya city-states made conquest a challenge. Spanish conquistadors only managed to establish colonies with the aid of former Aztec warriors and other Mesoamerican allies. Historically, the Maya had disappeared into the rainforest to escape undesirable political or environmental situations and continued to use tactical migration as another form of resistance. Their susceptibility to New World diseases such as typhus, measles, smallpox, and influenza decimated the Maya population.
7. Colonizations
Authors: Restall Matthew , Solari Amara
Published: October 2020

“Colonizations” charts the invasions and dislocations experienced on an unprecedented scale by the Maya peoples since the sixteenth century. The Maya area is carved up among five nation-states—Mexico, Guatemala, Belize, Honduras, and El Salvador. Agricultural centers such as Guatemala experienced slavery and exploitation in the nineteenth century, and in the latter half of the twentieth century, Mayas in Guatemala were subject to a campaign of violence and genocide. Their mystery has long entranced scholars of the Maya, giving rise to some extreme theories, including extraterrestrial involvement in Maya civilization. However, Maya history is a story not only of victimization, but also of adaptation and survival.
1. The three ages of silent film
Authors: Kornhaber Donna
Published: October 2020

“The three ages of silent film” charts the three commonly recognized periods of silent film: early, transitional, and classical. Changes in distribution after the early period shifted film’s role from a technological attraction presented as a transient fairground or vaudeville entertainment to a mode of storytelling presented in a fixed location in a nickelodeon or picture palace. This led to longer films with more complex composition and storytelling. The first film companies’ attempts to control the markets were circumvented by producers setting up West Coast studios. While European studios had a strong artistic influence that continued throughout the era, many struggled financially after the First World War.
5. The secret afterlife of silent film
Authors: Kornhaber Donna
Published: October 2020

The year 1929 is often seen as marking the end of silent film. “The secret afterlife of silent film” questions this date, demonstrating how that year only signaled the end of production in major studios in the United States. Once the technology for synchronization and amplification became available, the transition to sound in the motion picture industry was smoother than is often depicted. Silent film production continued in pockets around the globe until nearly the middle of the century, as did silent film exhibition. Elements of silent film persist even in the early twenty-first century, from avant-garde to animated films. Silent film is still beloved by critics and cinephiles, and the innovations of the silent period arguably contribute to the ongoing appeal of cinema itself.
Soft Matter: A Very Short Introduction
Authors: McLeish Tom
Published: October 2020

Soft Matter: A Very Short Introduction explores the field of soft matter, looking beneath the appearances of matter into its inner structure. Drawing on physics, chemistry, mathematics, and engineering, soft matter science links fundamental scientific ideas to everyday phenomena such as ‘inkiness’ and ‘stickiness’, with a rich history and philosophy. It studies materials such as polymers, colloids, liquid crystals, and foams. This VSI shows how Brownian Motion—the random molecular motion underlying ‘heat’—is an underpinning principle of soft matter. From hair conditioners to honey, it discusses how common characteristics of these materials shape their behaviour and applications.
4. Gelification and soapiness
Authors: McLeish Tom
Published: October 2020

‘Gelification and soapiness’ looks at the third class of soft matter: ‘self-assembly’. Like the colloids of inks and clays, and the polymers of plastics and rubbers, ‘self-assembled’ soft matter also emerges as a surprising consequence of Brownian motion combined with weak intermolecular forces. Like them, it also leads to explanations of a very rich world of materials and phenomena, such as gels, foams, soaps, and ultimately to many of the structures of biological life. There is an important distinction that needs to be made between one-dimensional and two-dimensional self-assembly.
5. Pearliness
Authors: McLeish Tom
Published: October 2020

‘Pearliness’ focuses on the soft matter class of ‘liquid crystals’ and considers a new ‘phase’ of matter: the ‘nematic’ state. The liquid crystal molecules are built of many atoms; they are mesoscopic objects. Their essential structure lies therefore in their overall rod-like shape, not in their specific atomistic constituents. In consequence, nematic behaviour is universal—there are many examples of molecules which form a nematic state. How do ideas from superconductivity and particle physics theory provide a conceptual framework for the theoretical physics of liquid crystals? There is another class of liquid crystals known as ‘smectic’ which are important to consider in this topic.
1. Subaltern knowledges
Authors: Young Robert J. C.
Published: October 2020

‘Subaltern knowledges’ discusses subaltern knowledges by looking at the perspectives of refugees. The terms ‘postcolonial’ and ‘decolonial’ signal the presence of the insurgent knowledges that come from the peripheries, from the indigenous, the marginalized, the dispossessed, and seek to transform the terms and values under which people live. Early interest in subalternity focused on subaltern consciousness but expanded to include divergent knowledges. Such knowledges are produced not just by subordinated groups with their individual cultures and histories but are also articulated in their different languages.
10. Ecology and indigeneity
Authors: Young Robert J. C.
Published: October 2020

‘Ecology and indigeneity’ assesses how postcolonial studies have shifted in emphasis from colonial history of exploitation colonies to those where the settler colonists themselves were the ones who achieved independence. This has led to an increasing focus on the relation between settlers and indigenous peoples of settler colonies whose land was appropriated or is being destroyed through resource extraction. A concern for ecology, particularly in the context of its destruction by modern industrial capitalism and its products, has also led to a different awareness of the richness of the traditions of indigenous people. Indigenous ecopolitics can be studied the examples of the Chipko movement in India and Greenbelt Movement in Kenya.
11. Translation
Authors: Young Robert J. C.
Published: October 2020

‘Translation’ explores the concept of translation which reflects the central conceptual and political dynamic of postcolonialism. Translating a text from one language to another transforms its material identity. Transforming an indigenous culture into the subordinated culture of a colonial regime or sovereign settler colony, or superimposing the colonial apparatus into which all aspects of the original culture have to be reconstructed operate as processes of translational dematerialization and reconstruction. Translation is an intercultural communication, but it also always involves questions of power relations and forms of domination. Colonized people must therefore retranslate themselves and their cultures; Frantz Fanon’s politics of translation offer a means to political empowerment and social transformation.
Defining Core Competencies for Epidemiologists in Academic Settings to Tackle Tomorrow’s Health Research Challenges: A Structured, Multinational Effort
Authors: Abraham Alison , Gille Doreen , Puhan Milo A , ter Riet Gerben , von Wyl Viktor ,   for the International Consortium on Teaching Epidemiology
Published: October 2020

Only a few efforts have been made to define core competencies for epidemiologists working in academic settings. Here we describe a multinational effort to define competencies for epidemiologists, who are increasingly facing emerging and potentially disruptive technological and societal health trends in academic research. During a 1.5-year period (2017–2019), we followed an iterative process that aimed to be inclusive and multinational to reflect the various perspectives of a diverse group of epidemiologists. Competencies were developed by a consortium in a consensus-oriented process that spanned 3 main activities: 2 in-person interactive meetings held in Amsterdam, the Netherlands, and Zurich, Switzerland, and an online survey. In total, 93 meeting participants from 16 countries and 173 respondents from 19 countries contributed to the development of 31 competencies. These 31 competencies included 14 on “developing a scientific question” and “study planning,” 12 on “study conduct and analysis,” 3 on “overarching competencies,” and 2 on “communication and translation.” The process described here provides a consensus-based framework for defining and adapting the field. It should initiate a continuous process of thinking about competencies and the implications for teaching epidemiology to ensure that epidemiologists working in academic settings are well prepared for today’s and tomorrow’s health research.
Genome-Wide Gene-by-Smoking Interaction Study of Chronic Obstructive Pulmonary Disease
Authors: Kim Woori , Prokopenko Dmitry , Sakornsakolpat Phuwanat , Hobbs Brian D , Lutz Sharon M , Hokanson John E , Wain Louise V , Melbourne Carl A , Shrine Nick , Tobin Martin D , Silverman Edwin K , Cho Michael H , Beaty Terri H
Published: October 2020

Risk of chronic obstructive pulmonary disease (COPD) is determined by both cigarette smoking and genetic susceptibility, but little is known about gene-by-smoking interactions. We performed a genome-wide association analysis of 179,689 controls and 21,077 COPD cases from UK Biobank subjects of European ancestry recruited from 2006 to 2010, considering genetic main effects and gene-by-smoking interaction effects simultaneously (2-degrees-of-freedom (df) test) as well as interaction effects alone (1-df interaction test). We sought to replicate significant results in COPDGene (United States, 2008–2010) and SpiroMeta Consortium (multiple countries, 1947–2015) data. We considered 2 smoking variables: 1) ever/never and 2) current/noncurrent. In the 1-df test, we identified 1 genome-wide significant locus on 15q25.1 (cholinergic receptor nicotinic β4 subunit, or CHRNB4) for ever- and current smoking and identified PI*Z allele (rs28929474) of serpin family A member 1 (SERPINA1) for ever-smoking and 3q26.2 (MDS1 and EVI1 complex locus, or MECOM) for current smoking in an analysis of previously reported COPD loci. In the 2-df test, most of the significant signals were also significant for genetic marginal effects, aside from 16q22.1 (sphingomyelin phosphodiesterase 3, or SMPD3) and 19q13.2 (Egl-9 family hypoxia inducible factor 2, or EGLN2). The significant effects at 15q25.1 and 19q13.2 loci, both previously described in prior genome-wide association studies of COPD or smoking, were replicated in COPDGene and SpiroMeta. We identified interaction effects at previously reported COPD loci; however, we failed to identify novel susceptibility loci.
Social work praxis in policy: Reflections from India
Authors: Sinha Ruchi , Juvva Srilatha
Published: October 2020

Viewing social work as a discipline gives primary attention to theories and perspectives, whereas viewing it as a profession places emphasis on practice and skills. It is assumed that theoretical frames enable a shift from particularities to the glocal view, thus ensuring pluralism. While it is hinted that practice embedded in ‘methods of social work’ is limited and a prisoner of historical practice realms, what one misses in these myopic distinctions is that, in social work the ‘centrality’ of person/client is non-negotiable. These newer conceptualisations embrace ‘in situations’ and radical perspectives across all methods of social work. Methods of social work provide the base to traverse the micro–macro linkages and ensure policy focus on individuals, structure, systems, cultural norms and its consequent impact. Praxis of the methods is imperative to make policies relevant. This article presents the robustness of methods in firming policies, for addressing situations of exclusion and powerlessness, with the values of inclusion and empowerment. Drawing on the Bordieu’s fields of power, capital and habitus, the article elucidates the application of methods of social work in a neo-liberal world to challenge structures that perpetuate inequity and translates the operationalisation of individual agency.
Comparison of Household Transmission of Influenza Virus From Index Patients Treated With Baloxavir Marboxil or Neuraminidase Inhibitors: A Health Insurance Claims Database Study
Authors: Komeda Takuji , Takazono Takahiro , Hosogaya Naoki , Ogura Eriko , Fujiwara Masakazu , Miyauchi Hideyuki , Ajisawa Yoshikazu , Iwata Shinpei , Watanabe Hideaki , Honda Keiichi , Kitanishi Yoshitake , Hara Kanae , Mukae Hiroshi
Published: October 2020

Background

Baloxavir marboxil (baloxavir) is expected to reduce influenza transmission by rapid reduction of viral load. The incidence of household transmission was compared between index patients (IPs) treated with baloxavir and those treated with neuraminidase inhibitors.

Methods

Using a Japanese claims database, the first family members with influenza diagnosis during the 2018–2019 influenza season were identified as IPs, and the diagnosis date was designated day 1. According to the anti-influenza drug dispensed to the IP, their families were classified into the oral baloxavir group and 3 controls: oral oseltamivir group (a primary control), inhaled zanamivir group, and inhaled laninamivir group. A household transmission was defined as influenza diagnosed for any non-IP family members during days 3−8. The incidence of household transmission was compared between groups using a logistic regression model adjusting backgrounds of IPs.

Results

The proportion of families with household transmission was 17.98% (15 226 of 84 672) in the baloxavir group and 24.16% (14 983 of 62 004) in the oseltamivir group. The covariate-adjusted odds ratio (oseltamivir/baloxavir) was 1.09 (95% confidence interval [95% CI], 1.05–1.12), which indicated significantly lower incidence in the baloxavir group. The adjusted odds ratios (controls/baloxavir) against zanamivir and laninamivir were 0.93 (95% CI, .89–.97) and 0.99 (95% CI, .96–1.02), respectively.

Conclusions

Baloxavir may contribute to reduction in household transmission compared with oseltamivir. In comparison between baloxavir and inhalants, a similar reduction was not shown and it might be due to unmeasured confounding by administration route differences.
Risk Factors for Testing Positive for Severe Acute Respiratory Syndrome Coronavirus 2 in a National United States Healthcare System
Authors: Fan Vincent S , Dominitz Jason A , Eastment McKenna C , Locke Emily R , Green Pamela , Berry Kristin , O’Hare Ann M , Shah Javeed A , Crothers Kristina , Ioannou George N
Published: October 2020

Background

Identifying risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection could help health systems improve testing and screening strategies. The aim of this study was to identify demographic factors, comorbid conditions, and symptoms independently associated with testing positive for SARS-CoV-2.

Methods

This was an observational cross-sectional study at the Veterans Health Administration, including persons tested for SARS-CoV-2 nucleic acid by polymerase chain reaction (PCR) between 28 February and 14 May 2020. Associations between demographic characteristics, diagnosed comorbid conditions, and documented symptoms with testing positive for SARS-CoV-2 were measured.

Results

Of 88 747 persons tested, 10 131 (11.4%) were SARS-CoV-2 PCR positive. Positivity was associated with older age (≥80 vs <50 years: adjusted odds ratio [aOR], 2.16 [95% confidence interval {CI}, 1.97–2.37]), male sex (aOR, 1.45 [95% CI, 1.34–1.57]), regional SARS-CoV-2 burden (≥2000 vs <400 cases/million: aOR, 5.43 [95% CI, 4.97–5.93]), urban residence (aOR, 1.78 [95% CI, 1.70–1.87]), black (aOR, 2.15 [95% CI, 2.05–2.26]) or American Indian/Alaska Native Hawaiian/Pacific Islander (aOR, 1.26 [95% CI, 1.05–1.52]) vs white race, and Hispanic ethnicity (aOR, 1.52 [95% CI, 1.40–1.65]). Obesity and diabetes were the only 2 medical conditions associated with testing positive. Documented fevers, chills, cough, and diarrhea were also associated with testing positive. The population attributable fraction of positive tests was highest for geographic location (35.3%), followed by demographic variables (27.1%), symptoms (12.0%), obesity (10.5%), and diabetes (0.4%).

Conclusions

The majority of positive SARS-CoV-2 tests were attributed to geographic location, demographic characteristics, and obesity, with a minor contribution of chronic comorbid conditions.
Liquid Biopsy for Invasive Mold Infections in Hematopoietic Cell Transplant Recipients With Pneumonia Through Next-Generation Sequencing of Microbial Cell-Free DNA in Plasma
Authors: Hill Joshua A , Dalai Sudeb C , Hong David K , Ahmed Asim A , Ho Carine , Hollemon Desiree , Blair Lily , Maalouf Joyce , Keane-Candib Jacob , Stevens-Ayers Terry , Boeckh Michael , Blauwkamp Timothy A , Fisher Cynthia E
Published: October 2020

Background

Noninvasive diagnostic options are limited for invasive mold infections (IMIs). We evaluated the performance of a plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary IMI after hematopoietic cell transplant (HCT).

Methods

We retrospectively assessed the diagnostic performance of plasma mcfDNA-Seq next-generation sequencing in 114 HCT recipients with pneumonia after HCT who had stored plasma obtained within 14 days of diagnosis of proven/probable Aspergillus IMI (n = 51), proven/probable non-Aspergillus IMI (n = 24), possible IMI (n = 20), and non-IMI controls (n = 19). Sequences were aligned to a database including >400 fungi. Organisms above a fixed significance threshold were reported.

Results

Among 75 patients with proven/probable pulmonary IMI, mcfDNA-Seq detected ≥1 pathogenic mold in 38 patients (sensitivity, 51% [95% confidence interval {CI}, 39%–62%]). When restricted to samples obtained within 3 days of diagnosis, sensitivity increased to 61%. McfDNA-Seq had higher sensitivity for proven/probable non-Aspergillus IMI (sensitivity, 79% [95% CI, 56%–93%]) compared with Aspergillus IMI (sensitivity, 31% [95% CI, 19%–46%]). McfDNA-Seq also identified non-Aspergillus molds in an additional 7 patients in the Aspergillus subgroup and Aspergillus in 1 patient with possible IMI. Among 19 non-IMI pneumonia controls, mcfDNA-Seq was negative in all samples, suggesting a high specificity (95% CI, 82%–100%) and up to 100% positive predictive value (PPV) with estimated negative predictive values (NPVs) of 81%–99%. The mcfDNA-Seq assay was complementary to serum galactomannan index testing; in combination, they were positive in 84% of individuals with proven/probable pulmonary IMI.

Conclusions

Noninvasive mcfDNA-Seq had moderate sensitivity and high specificity, NPV, and PPV for pulmonary IMI after HCT, particularly for non-Aspergillus species.
Mediatization from Within: A Plea for Emic Approaches to Media-Related Social Change
Authors: Jansson André , Bengtsson Stina , Fast Karin , Lindell Johan
Published: October 2020

Based on a literature review, this article shows that current mediatization scholarship is characterized by what Pike (1967) refers to as etic accounts. These accounts forward theoretical categories on media-related social change to conclude that our age is characterized by deepened and expanded media reliance. However, such theoretical extrapolation takes place not from, but at the expense of, people’s lived experiences, that is, emic accounts of mediatization in everyday life. This article is an attempt to insert the etic/emic distinction to mediatization research in order to develop more reflexive and composite accounts. Drawing on examples from a representative survey and qualitative interviews conducted over twenty years, the article problematizes etic-oriented conceptions of mediatization. Emic analyses expose how perceptions of media reliance shift over time and thus underscore the need to develop research strategies that simultaneously consider the objective structures of the social (mediatized) world and subjective meaning-making structures.
Myasthenia is a poor prognostic factor for perioperative outcomes after robotic thymectomy for thymoma
Authors: Kumar Arvind , Asaf Belal Bin , Pulle Mohan Venkatesh , Puri Harsh Vardhan , Sethi Nitin , Bishnoi Sukhram
Published: October 2020

OBJECTIVES

The goal of this study was to compare the early and intermediate surgical outcomes, including the survival of those with and without myasthenic thymoma, following robotic thymectomy.

METHODS

This is a retrospective analysis of prospectively maintained data of 111 patients who underwent robotic thymectomy for thymoma over 7 years in a thoracic surgery centre in India. We performed a comparative analysis of demographics, intraoperative variables and postoperative outcomes including survival of those with and without myasthenic thymoma.

RESULTS

Of 111 patients, 68 patients were myasthenic and 43 were non-myasthenic. The need to resect surrounding structures and conversions was greater in the myasthenic group (P = 0.02, P = 0.04). Postoperative complications were significantly higher in the myasthenic group (P = 0.02). No differences were observed in intensive care unit stay, the need for postoperative ventilation and the hospital stay. On correlation, a higher Masaoka stage [odds ratio 1.96, 95% confidence interval (CI) 1.22–3.15] and an aggressive World Health Organization histological diagnosis (odds ratio 1.58, 95% CI 1.10–2.26) were more likely in patients with myasthenia gravis. A total of 7 deaths (6.3%) occurred during the median follow-up of 4.2 years, 5 among those with myasthenic thymoma and 2 among patients with non-myasthenic thymoma. Due to the small number of deaths, there is insufficient evidence to draw any conclusion about the effect of myasthenia gravis on survival after surgery (hazard ratio 0.51, 95% CI 0.09–2.71; P = 0.43).

CONCLUSIONS

The presence of myasthenia with thymoma is associated with more adjacent structure resection, higher postoperative complications and more conversions. The use of robotic surgery for thymoma resection in patients with myasthenia could not overcome the early postoperative problems related to myasthenia gravis.
Cardiopulmonary bypass increases endothelial dysfunction after pulmonary ischaemia-reperfusion in an animal model
Authors: Selim Jean , Hamzaoui Mouad , Boukhalfa Inès , Djerada Zoubir , Chevalier Laurence , Piton Nicolas , Genty Damien , Besnier Emmanuel , Clavier Thomas , Dumesnil Anaïs , Renet Sylvanie , Mulder Paul , Doguet Fabien , Tamion Fabienne , Veber Benoît , Richard Vincent , Baste Jean-Marc
Published: October 2020

OBJECTIVES

Endothelial dysfunction during ischaemia-reperfusion (IR) is a major cause of primary graft dysfunction during lung transplantation. The routine use of cardiopulmonary bypass (CPB) during lung transplantation remains controversial. However, the contribution of CPB to pulmonary endothelial dysfunction remains unclear. The objective was to investigate the impact of CPB on endothelial dysfunction in a lung IR rat model.

METHODS

Rats were allocated to 4 groups: (i) Sham, (ii) IR, (iii) CPB and (iv) IR-CPB. The primary outcome was the study of pulmonary vascular reactivity by wire myograph. We also assessed glycocalyx degradation by enzyme-linked immunosorbent assay and electron microscopy and both systemic and pulmonary inflammation by enzyme-linked immunosorbent assay and immunohistochemistry. Rats were exposed to 45 min of CPB and IR. We used a CPB model allowing femoro-femoral support with left pulmonary hilum ischaemia for IR.

RESULTS

Pulmonary endothelium-dependent relaxation to acetylcholine was markedly reduced in the IR-CPB group (10.7 ± 9.1%) compared to the IR group (50.5 ± 5.2%, P < 0.001), the CPB group (54.1 ± 4.7%, P < 0.001) and the sham group (80.8 ± 6.7%, P < 0.001), suggesting that the association of pulmonary IR and CPB increases endothelial dysfunction. In IR-CPB, IR and CPB groups, vasorelaxation was completely abolished when inhibiting nitric oxide synthase, suggesting that this relaxation process was mainly mediated by nitric oxide. We observed higher syndecan-1 plasma levels in the IR-CPB group in comparison with the other groups, reflecting an increased degradation of glycocalyx. We also observed higher systemic inflammation in the IR-CPB group as shown by the increased plasma levels of IL-1β, IL-10.

CONCLUSIONS

CPB significantly increased the IR-mediated effects on pulmonary endothelial dysfunction. Therefore, the use of CPB during lung transplantation could be deleterious, by increasing endothelial dysfunction.
Plant components affect bacterial biofilm development by altering their cell surface physicochemical properties: a predictability study using Actinomyces naeslundii
Authors: Wang Yi , Samaranayake Lakshman P , Dykes Gary A
Published: October 2020

We hypothesized that the initial events leading to biofilm formation by bacteria, in general, are predominantly mediated by cell surface physicochemical interactions, and that natural products can impact the process by altering cell surface physicochemical properties. We exemplified this phenomenon using Actinomyces naeslundii as the model organism, and using tea products to modify its cell surface physicochemical properties. To test the hypothesis, a non-linear multiple regression model incorporating a normal distribution curve was constructed to explain the impact of tea extracts on the physiochemical processes of biofilm formation by A. naeslundii. The model utilized tea extract-induced changes in cell surface physicochemical properties as independent variables, and the corresponding biofilm formation as a dependent variable. Five different tea extracts were used to treat A. naeslundii, and their impact on the cell surface hydrophobicity, charge, auto-aggregation, attachment and biofilm formation on four different hard surfaces were measured and the data were used to construct the model. The established model was then tested in independent experiments involving other plant extracts and purified phytochemicals. Experimental results showed that the tea extracts significantly reduced cell surface hydrophobicity (by up to 21.3%), increased cell surface charge and auto-aggregation (by up to 4.5 mV and 14.9%, respectively), inhibited attachment (by 0.6–2.5 log CFU cm−2) and affected biofilm formation (by up to 0.6 log CFU cm−2). The model indicated that both cell surface hydrophobicity and charge played an important role in bacterial auto-aggregation and attachment, and that the latter two phenomena significantly correlated with subsequent biofilm development. The accuracy of the model construct was approximately 64%. This modelling approach can be employed for other microbial colonization systems to predict biofilm formation, and to study the impact of cell surface physicochemical properties in biofilm development.
Three-dimensional forward modelling of gravity field vector and its gradient tensor using the compact difference schemes
Authors: Pan Kejia , Zhang Zhihao , Hu Shuanggui , Ren Zhengyong , Guo Rongwen , Tang Jingtian
Published: October 2020

The traditional gravity forward modelling methods for solving partial differential equations (PDEs) only can yield second-order accuracy. When computing the gravity field vector and gradient tensor from the obtained potential, those numerical differentiation approaches will inevitably lose accuracy. To mitigate this issue, we propose an efficient and accurate 3-D forward modelling algorithm based on a fourth-order compact difference scheme. First, a 19-point fourth-order compact difference scheme with general meshsizes in x-, y- and z-directions is adopted to discretize the governing 3-D Poisson’s equation. The resulting symmetric positive-definite linear systems are solved by the pre-conditioned conjugate gradient algorithm. To obtain the first-order (i.e. the gravity field vector) and second-order derivatives (i.e. the gravity gradient tensor) with fourth-order accuracy, we seek to solve a sequence of tridiagonal linear systems resulting from the above mentioned finite difference discretization by using fast Thomas algorithm. Finally, two synthetic models and a real topography relief are used to verify the accuracy of our method. Numerical results show that our method can yield a nearly fourth-order accurate approximation not only to the gravitational potential, but also to the gravity field vector and its gradient tensor, which clearly demonstrates its superiority over the traditional PDE-based methods.
Investigation of acidic free-glycans in urine and their alteration in cancer
Authors: Hanzawa Ken , Tanaka-Okamoto Miki , Murakami Hiroko , Mukai Mikio , Takahashi Hidenori , Omori Takeshi , Ikezawa Kenji , Ohkawa Kazuyoshi , Ohue Masayuki , Miyamoto Yasuhide
Published: October 2020

Alterations to glycans in cancer patients have been used to identify novel tumor biomarkers. Most of these studies have focused on protein glycosylation but less attention has been paid to free-glycans. Here, we analyzed acidic free-glycans in the urine of cancer patients to identify novel tumor marker candidates. Specifically, urine samples were collected from patients with gastric cancer, pancreatic cancer and cholangiocarcinoma as well as normal controls. The free-glycans were extracted from creatinine-adjusted urine and fluorescently labeled with 2-aminopyridine. Initially, we performed profiling of urinary free-glycans by high-performance liquid chromatography and mass spectrometry with enzymatic and chemical degradation. More than 100 glycans, including novel structures, were identified. The chromatographic peaks suggested some of these glycans were present at elevated levels in cancer patients. To verify cancer-associated alterations, we compared the glycan levels between cancer patients and normal controls by selected reaction monitoring. Representative structures of glycans with elevated levels in cancer patients included the following: small glycans related to sialyllactose; sialyl Lewis X; lactose- and N-acetyllactosamine (LacNAc) type-II-core glycans with LacNAc (type-I or II)-extensions and modifications of α1,3/4-fucose and/or 6-sulfate on the Glc/GlcNAc; free-N-glycans containing sialylation or β1,6-branch of 6-sulfo Lewis X; novel NeuAcα2-3Galβ1-4(+/−Fucα1-3) Xylα1-3Glc glycans. Our results provide further insight into urinary free-glycans and suggest the potential utility of these compounds as tumor markers.
Economic evaluation of interventions to address undernutrition: a systematic review
Authors: Ramponi Francesco , Tafesse Wiktoria , Griffin Susan
Published: October 2020

Strategies to address undernutrition in low- and middle-income countries (LMICs) include various interventions implemented through different sectors of the economy. Our aim is to provide an overview of published economic evaluations of such interventions and to compare and contrast evaluations of interventions in different areas. We reviewed economic evaluations of nutrition interventions in LMICs published since 2015 and/or included in the Tufts Global registry or Disease Control Priorities 3rd edition. We categorized the studies by intervention type (preventive; therapeutic; fortification; delivery platforms), nutritional deficiency addressed and characteristics of the economic evaluation (e.g. type of model, costs and outcomes included). Of the 62 economic evaluations identified, 56 (90%) were cost-effectiveness analyses. Twenty-two (36%) evaluations investigated fortification and 23 (37%) preventive interventions. Forty-three percent of the evaluations of preventive interventions did not include a model, whereas most of fortification strategies used the same reference model. We identified different trends in cost categories and inclusion of health and non-health outcomes across evaluations in the four different topic areas. To illustrate the implications of such trends for decision-making, we compared a set of studies evaluating alternative strategies to combat zinc deficiency. We showed that the use of ‘off-the-shelf’ models and tools can potentially conceal what outcomes and costs and value judgements are used. Comparing interventions across different areas is fundamental to assist decision-makers in developing their nutrition strategy. Systematic differences in the economic evaluations of interventions delivered within and outside the health sector can undermine the ability to prioritize alternative nutrition strategies.
Demographic history and admixture dynamics in African Sahelian populations
Authors: Černý Viktor , Fortes-Lima Cesar , Tříska Petr
Published: October 2020

The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
Impact of immunohistochemistry-based molecular subtype on predicting chemotherapy response and survival in patients with T1 stage bladder cancer after bladder-preserving treatment
Authors: Lu Jiangli , Zhang Yijun , Wu Chenyan , Chu Chengbiao , Liu Zhuowei , Cao Yun
Published: October 2020

Objective

To explore the immunohistochemistry-based molecular subtypes of bladder cancer, and their impact on the prognosis and the chemotherapy response between gemcitabine plus cisplatin intra-arterial chemotherapy and epirubicin-inducted intravesical chemotherapy, in patients with T1 stage bladder cancer after bladder-preserving treatment.

Methods

One hundred and seventy-six patients with T1 stage bladder cancer were selected for this study. Thirty-three patients underwent radical cystectomy, 43 received gemcitabine plus cisplatin intra-arterial chemotherapy and 100 received intravesical chemotherapy. The markers labeled with luminal (GATA3, Uroplakin II, CK20) and basal (CK5/6, CK14, CD44) phenotypes were chosen as candidate markers.

Results

One hundred and seventy-six patients were divided into 76 patients as basal/squamous (BASQ), 45 as the luminal A and 55 as the luminal B. Compared with the luminal B and BASQ tumors, the luminal A tumors showed a trend for better recurrence-free survival (P = 0.105) and progression-free survival (P = 0.093). The combination of CK20 and GATA3 was practical to identify the molecular phenotypes with total 84.9% accuracy and significantly associated with recurrence-free survival (P = 0.025) and progression-free survival (P = 0.004). The patient with BASQ tumors who received intravesical chemotherapy showed a trend for worse progression-free survival than the patient who received gemcitabine plus cisplatin intra-arterial chemotherapy or radical cystectomy. Furthermore, the patients with BASQ tumors experienced a significant improvement in progression-free survival after gemcitabine plus cisplatin intra-arterial chemotherapy compared with the patients who received intravesical chemotherapy (P = 0.011).

Conclusions

The immunohistochemistry-based molecular subtypes could predict the patient’s prognosis and clinically different chemotherapeutic survival outcomes in patients with T1 stage bladder cancer after bladder-preserving treatment.
Bayesian AGN Decomposition Analysis for SDSS spectra: a correlation analysis of [O iii] λ5007 outflow kinematics with AGN and host galaxy properties
Authors: Sexton Remington O , Matzko William , Darden Nicholas , Canalizo Gabriela , Gorjian Varoujan
Published: October 2020

We present Bayesian active galactic nucleus (AGN) Decomposition Analysis for Sloan Digital Sky Survey (SDSS) Spectra, an open source spectral analysis code designed for automatic detailed deconvolution of AGN and host galaxy spectra, implemented in python, and designed for the next generation of large-scale surveys. The code simultaneously fits all spectral components, including power-law continuum, stellar line-of-sight velocity distribution, Fe ii emission, as well as forbidden (narrow), permitted (broad), and outflow emission line features, all performed using Markov chain Monte Carlo to obtain robust uncertainties and autocorrelation analysis to assess parameter convergence. Our code also utilizes multiprocessing for batch fitting large samples of spectra while efficiently managing memory and computation resources and is currently being used in a cluster environment to fit thousands of SDSS spectra. We use our code to perform a correlation analysis of 63 SDSS type 1 AGNs with evidence of strong non-gravitational outflow kinematics in the [O iii] λ5007 emission feature. We confirm findings from previous studies that show the core of the [O iii] profile is a suitable surrogate for stellar velocity dispersion σ*, however there is evidence that the core experiences broadening that scales with outflow velocity. We find sufficient evidence that σ*, [O iii] core dispersion, and the non-gravitational outflow dispersion of the [O iii] profile form a plane whose fit results in a scatter of ∼0.1 dex. Finally, we discuss the implications, caveats, and recommendations when using the [O iii] dispersion as a surrogate for σ* for the MBH−σ* relation.
Influence of the input-stage architecture on the in-laboratory test of a mid-infrared interferometer: application to the ALOHA up-conversion interferometer in the L band
Authors: Magri Julie , Lehmann Lucien , Grossard Ludovic , Delage Laurent , Reynaud François , Chauvet Mathieu , Bassignot Florent , Krawczyk Rodolphe , Le Duigou Jean-Michel
Published: October 2020

In the framework of the Astronomical Light Optical Hybrid Analysis (ALOHA) laboratory mid-infrared (MIR) up-conversion fibred interferometer in the L band, we report on the influence of the input-stage architecture. Using an amplitude division set-up in the visible or near-infrared is a straightforward choice in most cases. In the MIR context, the results are slightly different and we show that a wavefront division set-up is needed. These in-laboratory principle experiments allow us to measure a reliable 88 per cent instrumental contrast with high flux and to obtain fringes from faint sources at 3.5 μm with a spectral bandwith of 37 nm converted to 817 nm. An equivalent limiting L-band magnitude around 3.9, equivalent to 3.0 fW nm−1, could be demonstrated on 1 m class telescopes. This opens the possibility of planning future on-sky tests at the Center for High Angular Resolution Astronomy (CHARA) array and of predicting the performance attained.
Streaming instability on different scales – I. Planetesimal mass distribution variability
Authors: Rucska J J , Wadsley J W
Published: October 2020

We present numerical simulations of dust clumping and planetesimal formation initiated by the streaming instability (SI) with self-gravity. We examine the variability in the planetesimal formation process by employing simulation domains with large radial and azimuthal extents and a novel approach of re-running otherwise identical simulations with different random initializations of the dust density field. We find that the planetesimal mass distribution and the total mass of dust that is converted into planetesimals can vary substantially between individual small simulations and within the domains of larger simulations. Our results show that the non-linear nature of the developed SI introduces substantial variability in the planetesimal formation process that has not been previously considered and suggests larger scale dynamics may affect the process.
FlyBase: updates to theDrosophila melanogasterknowledge base
Authors: Larkin Aoife , Marygold Steven J , Antonazzo Giulia , Attrill Helen , dos Santos Gilberto , Garapati Phani V , Goodman Joshua L , Gramates L Sian , Millburn Gillian , Strelets Victor B , Tabone Christopher J , Thurmond Jim ,   FlyBase Consortium, Perrimon Norbert , Gelbart Susan Russo , Agapite Julie , Broll Kris , Crosby Madeline , dos Santos Gilberto , Falls Kathleen , Gramates L Sian , Jenkins Victoria , Longden Ian , Matthews Beverley , Sutherland Carol , Tabone Christopher J , Zhou Pinglei , Zytkovicz Mark , Brown Nick , Antonazzo Giulia , Attrill Helen , Garapati Phani , Larkin Aoife , Marygold Steven , McLachlan Alex , Millburn Gillian , Pilgrim Clare , Ozturk-Colak Arzu , Trovisco Vitor , Kaufman Thomas , Calvi Brian , Goodman Josh , Strelets Victor , Thurmond Jim , Cripps Richard , Lovato TyAnna
Published: October 2020

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays (‘ribbons’) of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants
Authors: Zhao Lianhe , Wang Jiajia , Li Yanyan , Song Tingrui , Wu Yang , Fang Shuangsang , Bu Dechao , Li Hui , Sun Liang , Pei Dong , Zheng Yu , Huang Jianqin , Xu Mingqing , Chen Runsheng , Zhao Yi , He Shunmin
Published: October 2020

NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.
The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase
Authors: Cieśla Małgorzata , Turowski Tomasz W , Nowotny Marcin , Tollervey David , Boguta Magdalena
Published: October 2020

The biogenesis of eukaryotic RNA polymerases is poorly understood. The present study used a combination of genetic and molecular approaches to explore the assembly of RNA polymerase III (Pol III) in yeast. We identified a regulatory link between Rbs1, a Pol III assembly factor, and Rpb10, a small subunit that is common to three RNA polymerases. Overexpression of Rbs1 increased the abundance of both RPB10 mRNA and the Rpb10 protein, which correlated with suppression of Pol III assembly defects. Rbs1 is a poly(A)mRNA-binding protein and mutational analysis identified R3H domain to be required for mRNA interactions and genetic enhancement of Pol III biogenesis. Rbs1 also binds to Upf1 protein, a key component in nonsense-mediated mRNA decay (NMD) and levels of RPB10 mRNA were increased in a upf1Δ strain. Genome-wide RNA binding by Rbs1 was characterized by UV cross-linking based approach. We demonstrated that Rbs1 directly binds to the 3′ untranslated regions (3′UTRs) of many mRNAs including transcripts encoding Pol III subunits, Rpb10 and Rpc19. We propose that Rbs1 functions by opposing mRNA degradation, at least in part mediated by NMD pathway. Orthologues of Rbs1 protein are present in other eukaryotes, including humans, suggesting that this is a conserved regulatory mechanism.