bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary Perspectives on Germline-Restricted Chromosomes in Flies (Diptera)
Authors: Hodson Christina N , Ross Laura
Published: April 2021

In some eukaryotes, germline soma differentiation involves elimination of parts of the genome from somatic cells. The portions of the genome restricted to the germline often contain genes that play a role in development and function of the germline. Lineages with germline-restricted DNA are taxonomically diverse, and the size of the germline-restricted genome varies substantially. Unfortunately, few of these lineages have been studied in detail. As a result, we understand little about the general evolutionary forces that drive the origin and maintenance of germline-restricted DNA. One of the taxonomic groups where germline-restricted DNA has been poorly studied are the flies (Diptera). In three Dipteran families, Chironomidae, Cecidomyiidae, and Sciaridae, entire chromosomes are eliminated from somatic cells early in embryonic development. Germline-restricted chromosomes are thought to have evolved independently in the Dipteran families and their size, number, and transmission patterns vary between families. Although there is a wealth of cytological studies on these chromosomes in flies, almost no genomic studies have been undertaken. As a result, very little is known about how and why they evolved and what genes they encode. This review summarizes the literature on germline-restricted chromosomes in Diptera, discusses hypotheses for their origin and function, and compares germline-restricted DNA in Diptera to other eukaryotes. Finally, we discuss why Dipteran lineages represent a promising system for the study of germline-restricted chromosomes and propose future avenues of research on this topic.
Functional Analysis of the PUT3 Transcriptional Activator of the Proline Utilization Pathway in Saccharomyces cerevisiae
Authors: Etages Shelley Ann G des , Fahey Darlene A , Reece Richard J , Brandriss Marjorie C
Published: April 2021

Proline can serve as a nitrogen source for the yeast Saccharomyces cerevisiae when preferred sources of nitrogen are absent from the growth medium. PUT3, the activator of the proline utilization pathway, is required for the transcription of the genes encoding the enzymes that convert proline to glutamate. PUT3 is a 979 amino acid protein that constitutively binds a short DNA sequence in the promoters of its target genes, but does not activate their expression in the absence of induction by proline and in the presence of preferred sources of nitrogen. To understand how PUT3 is converted from an inactive to an active state, a dissection of its functional domains has been undertaken. Biochemical and molecular tests, domain swapping experiments, and an analysis of activator-constitutive and activator-defective mutant proteins indicate that PUT3 is dimeric and activates transcription with its negatively charged carboxyterminus, which does not appear to contain a proline-responsive domain. A mutation in the conserved central domain found in many fungal activators interferes with activation without affecting DNA binding or protein stability. Intragenic suppressors of the central domain mutation have been isolated and analyzed.
Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map
Authors: Johnson Stephen L , Gates Michael A , Johnson Michele , Talbot William S , Horne Sally , Baik Kris , Rude Sunny , Wong Jamie R , Postlethwait John H
Published: April 2021

The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.
Transmission-Ratio Distortion Through F1 Females at Chromosome 11 Loci Linked to Om in the Mouse DDK Syndrome
Authors: de Villena F Pardo-Manuel , Slamka C , Fonseca M , Naumova A K , Paquette J , Pannunzio P , Smith M , Verner A , Morgan K , Sapienza C
Published: April 2021

We determined the genotypes of >200 offspring that are survivors of matings between female reciprocal F1 hybrids (between the DDK and C57BL/6J inbred mouse strains) and C57BL/6J males at markers linked to the Ovum mutant (Om) locus on chromosome 11. In contrast to the expectations of our previous genetic model to explain the “DDK syndrome,” the genotypes of these offspring do not reflect preferential survival of individuals that receive C57BL/6J alleles from the F1 females in the region of chromosome 11 to which the Om locus has been mapped. In fact, we observe significant transmission-ratio distortion in favor of DDK alleles in this region. These results are also in contrast to the expectations of Wakasugi's genetic model for the inheritance of Om, in which he proposed equal transmission of DDK and non-DDK alleles from F1 females. We propose that the results of these experiments may be explained by reduced expression of the maternal DDK Om allele or expression of the maternal DDK Om allele in only a portion of the ova of F1 females
Vegetative Incompatibility in the het-6 Region of Neurospora crassa Is Mediated by Two Linked Genes
Authors: Smith M L , Micali O C , Hubbard S P , Mir-Rashed N , Jacobson D J , Glass N Louise
Published: April 2021

Non-self-recognition during asexual growth of Neurospora crassa involves restriction of heterokaryon formation via genetic differences at 11 het loci, including mating type. The het-6 locus maps to a 250-kbp region of LGIIL. We used restriction fragment length polymorphisms in progeny with crossovers in the het-6 region and a DNA transformation assay to identify two genes in a 25-kbp region that have vegetative incompatibility activity. The predicted product of one of these genes, which we designate het-6OR, has three regions of amino acid sequence similarity to the predicted product of the het-e vegetative incompatibility gene in Podospora anserina and to the predicted product of tol, which mediates mating-type vegetative incompatibility in N. crassa. The predicted product of the alternative het-6 allele, HET-6PA, shares only 68% amino acid identity with HET-6OR. The second incompatibility gene, un-24OR, encodes the large subunit of ribonucleotide reductase, which is essential for de novo synthesis of DNA. A region in the carboxylterminal portion of UN-24 is associated with incompatibility and is variable between un-24OR and the alternative allele un-24PA. Linkage analysis indicates that the 25-kbp un-24-het-6 region is inherited as a block, suggesting that a nonallelic interaction may occur between un-24 and het-6 and possibly other loci within this region to mediate vegetative incompatibility in the het-6 region of N. crassa.
The Cloning and Molecular Analysis of pawn-B in Paramecium tetraurelia
Authors: Haynes W John , Ling Kit-Yin , Preston Robin R , Saimi Yoshiro , Kung Ching
Published: April 2021

Pawn mutants of Paramecium tetraurelia lack a depolarization-activated Ca2+ current and do not swim backward. Using the method of microinjection and sorting a genomic library, we have cloned a DNA fragment that complements pawn-B (pwB/pwB). The minimal complementing fragment is a 798-bp open reading frame (ORF) that restores the Ca2+ current and the backward swimming when expressed. This ORF contains a 29-bp intron and is transcribed and translated. The translated product has two putative transmembrane domains but no clear matches in current databases. Mutations in the available pwB alleles were found within this ORF. The d4-95 and d4-96 alleles are single base substitutions, while d4-662 (previously pawn-D) harbors a 44-bp insertion that matches an internal eliminated sequence (IES) found in the wild-type germline DNA except for a single C-to-T transition. Northern hybridizations and RT-PCR indicate that d4-662 transcripts are rapidly degraded or not produced. A second 155-bp IES in the wild-type germline ORF excises at two alternative sites spanning three asparagine codons. The pwB ORF appears to be separated from a 5′ neighboring ORF by only 36 bp. The close proximity of the two ORFs and the location of the pwB protein as indicated by GFP-fusion constructs are discussed.
Visit-to-Visit Blood Pressure Variability and Incident Frailty in Older Adults
Authors: Rouch Laure , De Souto Barreto Philipe , Hanon Olivier , Vidal Jean-Sébastien , Amar Jacques , Andrieu Sandrine , Cestac Philippe , Rolland Yves , Vellas Bruno ,   MAPT/DSA Group, Vellas Bruno , Guyonnet Sophie , Carrié Isabelle , Brigitte Lauréane , Faisant Catherine , Lala Françoise , Delrieu Julien , Villars Hélène , Combrouze Emeline , Badufle Carole , Zueras Audrey , Andrieu Sandrine , Cantet Christelle , Morin Christophe , Van Kan Gabor Abellan , Dupuy Charlotte , Rolland Yves , Caillaud Céline , Ousset Pierre-Jean , Lala Françoise
Published: April 2021

This study aimed to determine whether visit-to-visit blood pressure (BP) variability (BPV) is associated with incident frailty. We included 1 394 nonfrail community-dwelling participants aged ≥70 years from the Multidomain Alzheimer Preventive Trial (MAPT) who underwent repeated clinical examinations, including BP and frailty, over a 5-year follow-up period. Systolic BPV (SBPV), diastolic BPV (DBPV), mean arterial pressure variability (MAPV), and pulse pressure variability (PPV) were evaluated using standard deviation (SD), coefficient of variation (CV), average real variability, successive variation, variation independent of mean, and residual SD. Incident frailty was assessed using the Fried phenotype. Cox proportional hazards models were used for the analyses. Higher SBPV was significantly associated with greater risk of frailty (1-SD increase of CV: hazard ratio [HR] = 1.18, 95% confidence interval [CI]: 1.02–1.36) after adjustment for demographics, systolic BP, antihypertensive drugs, body mass index, diabetes, ischemic heart disease, congestive heart failure, stroke, atrial fibrillation, MAPT randomization group, and frailty status. Similar results were observed with all indicators of variability. Higher PPV was associated with a greater risk of developing frailty over time (1-SD increase of CV: HR = 1.17, 95% CI: 1.01–1.35). DBPV and MAPV were not significantly associated with incident frailty. Higher SBPV and PPV were associated with greater risk of incident frailty. Our findings support the concept of BP physiological dysregulation underlying the frail state and suggest that BP instability could be an early marker of frailty.
Nursing Home Competition, Prices, and Quality: A Scoping Review and Policy Lessons
Authors: Yang Ou , Yong Jongsay , Scott Anthony
Published: April 2021

Background and Objectives

In recent years, countries have increasingly relied on markets to improve efficiency, contain costs, and maintain quality in aged care. Under the right conditions, competition can spur providers to compete by offering better prices and higher quality of services. However, in aged care, market failures can be extensive. Information about prices and quality may not be readily available and search costs can be high. This study undertakes a scoping review on competition in the nursing home sector, with an emphasis on empirical evidence in relation to how competition affects prices and quality of care.

Research Design and Methods

Online databases were used to identify studies published in the English language between 1988 and 2020. A total of 50 studies covering 9 countries are reviewed.

Results

The review finds conflicting evidence on the relationship between competition and quality. Some studies find greater competition leading to higher quality, others find the opposite. Institutional features such as the presence of binding supply restrictions on nursing homes and public reporting of quality information are important considerations. Most studies find greater competition tends to result in lower prices, although the effect is small.

Discussion and Implications

The literature offers several key policy lessons, including the relationship between supply restrictions and quality, which has implications on whether increasing subsidies can result in higher quality and the importance of price transparency and public reporting of quality.
Robust Performance of Spider Viscid Silk on Hairy and Smooth Insect Substrates
Authors: Alicea-Serrano Angela M , Onyak Ariel , Dhinojwala Ali , Blackledge Todd A
Published: April 2021

Spider viscid silk adheres to insects in orb webs and is a “smart-adhesive” that quickly changes droplet size, viscosity, and adhesiveness in response to atmospheric humidity. Different species of spiders “tune” water uptake to match the humidity of their foraging environments, achieving a similar “universal” viscosity that optimizes tradeoffs in spreading versus cohesive bulk energy needed to enhance adhesion. Too much water lowers viscosity so that the glue spreads well, but cohesive failure occurs easily, generating poor adhesion. However, the optimal viscosity model of adhesion is based on experiments using smooth glass. Here we test the hypothesis that a less viscous, “over-lubricated” glue, which shows poor adhesion on smooth glass, will be stickier on hairy insects because of its greater ability to spread across three-dimensional rough surfaces. We ran adhesion tests of the furrow spider (Larinioides cornutus [Clerck 1757]) viscid silk on honey bee (Apis mellifera) thorax, with and without hairs, in either high or medium humidity. Our results show that “over-lubricated” glue increases adhesion on hairy surfaces, performing equally as well as an optimally viscous glue.
Anthropogenic Alteration of Flow, Temperature, and Light as Life-History Cues in Stream Ecosystems
Authors: Perkin Elizabeth K , Wilson Matthew J
Published: April 2021

Life history events, from mating and voltinism to migration and emergence, are governed by external and historically predictable environmental factors. The ways humans have altered natural environments during the Anthropocene have created myriad and compounding changes to these historically predictable environmental cues. Over the past few decades, there has been an increased interest in the control temperature exerts on life history events as concern over climate change has increased. However, temperature is not the only life history cue that humans have altered. In stream ecosystems, flow and light serve as important life history cues in addition to temperature. The timing and magnitude of peak flows can trigger migrations, decreases in stream temperature may cause a stream insect to enter diapause, and photoperiod appears to prompt spawning in some species of fish. Two or more of these cues may interact with one another in complex and sometimes unpredictable ways. Large dams and increasing impervious cover in urban ecosystems have modified flows and altered the timing of spawning and migration in fish. Precipitation draining hot impervious surfaces increases stream temperature and adds variability to the general pattern of stream warming from climate change. The addition of artificial light in urban and suburban areas is bright enough to eliminate or dampen the photoperiod signal and has resulted in caddisfly emergence becoming acyclical. The resulting changes in the timing of life history events also have the potential to influence the evolutionary trajectory of an organism and its interactions with other species. This paper offers a review and conceptual framework for future research into how flow, temperature, and light interact to drive life history events of stream organisms and how humans have changed these cues. We then present some of the potential evolutionary and ecological consequences of altered life history events, and conclude by highlighting what we perceive to be the most pressing research needs.
How pharmacists perceive their professional identity: a scoping review and discursive analysis
Authors: Kellar Jamie , Singh Lachmi , Bradley-Ridout Glyneva , Martimianakis Maria Athina , van der Vleuten Cees P M , oude Egbrink Mirjam G A , Austin Zubin
Published: April 2021

Objectives

The objectives of this scoping review were to (a) explore how pharmacists perceive their professional roles and identities and (b) describe factors impacting which professional roles or identities pharmacists embody in different pharmacy practice settings.

Methods

A scoping review using a deductive approach was undertaken for this study. Systematic searches were conducted in five databases: Ovid MEDLINE, Ovid EMBASE, Ovid PsycINFO, EBSCO Cumulative Index to Nursing and Allied Health and Scopus (Elsevier). Key words searched included pharmacist, identity, professional role and one variations of these. Results were double-blind screened for relevance by two authors. Data extraction was facilitated by the web-based software platform COVIDENCE. Foucauldian critical discourse analysis was used to deconstruct how pharmacists perceive their professional roles and identities.

Key findings

In total, 21 701 articles were retrieved in the search. Following de-duplication and screening, 23 studies from 11 different countries were included. Five major identity themes were identified: Clinician, Dispenser, Business Person, Patient Counsellor and Physician Supporter. The dispenser identity was the most widespread, but it was viewed by many pharmacists as undesirable. The clinician identity also had a strong presence but was viewed as an identity that pharmacists aspire to embody.

Conclusions

This scoping review illustrates that pharmacists do not uniformly perceive themselves to be clinicians. A significant gap exists between the profession’s desired identity and that embodied by practicing pharmacists. The resulting dissonance may be a contributing factor to the lack of wide-scale practice change that the profession has been seeking for decades.
Dielectric breakdown sizes of conducting plates
Authors: Yang Mimi X , Yang Fuqian , Lee Sanboh
Published: April 2021

In this work, we propose mathematical formulations that detail the effect of the dielectric strength of dielectric material on the spatial distribution of electric field in an infinite space with a conducting plate. Using the dielectric strength of air as the maximum limit for the magnitude of electric field intensity and the equivalence of stored charge between two different zones, we determine the size of the dielectric breakdown region (the extended region with ionized material) for the conducting strip and the conducting disk charged to an electric voltage. The size of dielectric breakdown is proportional to the square of the applied voltage, and decreases with the increase of the width/radius of the conducting strip/disk.
Long-Term Trends of Planted Loblolly Pine Diameter Distribution Characteristics
Authors: Green P Corey
Published: April 2021

Diameter distributions are fundamental characteristics of stand structure. It is widely assumed that unthinned plantation loblolly pine (Pinus taeda L.) diameter distributions are unimodal and slightly skewed. In this work, the assumption of unimodality is formally tested and confirmed using 413 long-term permanent plots representing three generations of genetics and silviculture across the native range of loblolly pine in the southeastern United States. Approximately 96% of plot measurements had no significant evidence to reject the hypothesis of unimodality. While levels often significantly differed, similar developmental trends of skewness, kurtosis, and estimated Weibull parameters were observed despite the advances of genetics and silviculture. The results of the study indicate the continued need for a flexible distribution for characterizing diameter distributions in plantation loblolly pine.
Assessment of the confidence interval in the multivariable normal tissue complication probability model for predicting radiation-induced liver disease in primary liver cancer
Authors: Prayongrat Anussara , Srimaneekarn Natchalee , Sriswasdi Sira , Ito Yoichi M , Katoh Norio , Tamura Masaya , Dekura Yasuhiro , Toramatsu Chie , Khorprasert Chonlakiet , Amornwichet Napapat , Alisanant Petch , Hirata Yuichi , Hayter Anthony , Shirato Hiroki , Shimizu Shinichi , Kobashi Keiji
Published: April 2021

We developed a confidence interval-(CI) assessing model in multivariable normal tissue complication probability (NTCP) modeling for predicting radiation-induced liver disease (RILD) in primary liver cancer patients using clinical and dosimetric data. Both the mean NTCP and difference in the mean NTCP (ΔNTCP) between two treatment plans of different radiotherapy modalities were further evaluated and their CIs were assessed. Clinical data were retrospectively reviewed in 322 patients with hepatocellular carcinoma (n = 215) and intrahepatic cholangiocarcinoma (n = 107) treated with photon therapy. Dose–volume histograms of normal liver were reduced to mean liver dose (MLD) based on the fraction size-adjusted equivalent uniform dose. The most predictive variables were used to build the model based on multivariable logistic regression analysis with bootstrapping. Internal validation was performed using the cross-validation leave-one-out method. Both the mean NTCP and the mean ΔNTCP with 95% CIs were calculated from computationally generated multivariate random sets of NTCP model parameters using variance–covariance matrix information. RILD occurred in 108/322 patients (33.5%). The NTCP model with three clinical and one dosimetric parameter (tumor type, Child–Pugh class, hepatitis infection status and MLD) was most predictive, with an area under the receiver operative characteristics curve (AUC) of 0.79 (95% CI 0.74–0.84). In eight clinical subgroups based on the three clinical parameters, both the mean NTCP and the mean ΔNTCP with 95% CIs were able to be estimated computationally. The multivariable NTCP model with the assessment of 95% CIs has potential to improve the reliability of the NTCP model-based approach to select the appropriate radiotherapy modality for each patient.
Carving Out Space for Equitable Collaborative Research in Protracted Displacement
Authors: Shuayb Maha , Brun Cathrine
Published: April 2021

Research collaborations between global north and south have a long history in studies of forced migration, and discussions of power relations in such research relationships have existed for a long time. We are two researchers working across the global south–north divide, and this article reflects on our attempt to navigate the research industry amid the ‘Syrian refugee research complex’. We discuss our attempt to carve out a space for more equitable research collaborations across the north–south divide and between partners. We unpack the existing power dynamics and the systems attached to them, e.g. institutional constraints, funding regulations, budget restrictions, and residues of post-colonial power dynamics. We then reflect on how these dynamics help to maintain the north’s hegemony in the research and knowledge production cycle. We argue that collaborative research can gain from a reflective practice that focuses on the relational aspects involved in research. This can be achieved through a ‘friendship approach’ rather than ‘tick-the-box guidelines’.
Understanding Food-Related Well-Being in a Diaspora Situation: The Psychological and Social Dimensions
Authors: Al-Sayed Lubana , Bieling Claudia
Published: April 2021

Food and related practices have a substantial impact on the well-being of individuals. When people are forced to migrate, it is unclear how this affects and potentially reshapes their understanding of food-related well-being. By drawing upon 34 semi-structured interviews with Syrian refugees in Stuttgart, Germany, this article presents an in-depth investigation of the psychological and social dimensions of food-related well-being in a diaspora situation. Interview partners express a strong affinity to their past food-related life and a constant comparison between what they are used to and what is currently available to them in the new food environment. Moreover, participants articulate a low autonomy and weak environmental mastery over food choices, which plays out differently according to the stage of displacement. Food is important for building new bridges with the host community and expressing social identities. The insights gained from this research are useful to design strategies to promote the well-being of refugees.
Retroperitoneal cystic mass: a rare form of adrenal pheochromocytoma
Authors: Moez Rahoui , Ouanes Yassine , Sahnoun Wajih , Mokhtar Bibi , Dali Khaireddine Mrad , Sellami Ahmed , Ben Rhouma Sami , Nouira Yassine
Published: April 2021

Adrenal cysts are usually non-functional and asymptomatic. Cystic pheochromocytomas are a rare clinical entity and difficult to differentiate from simple cysts in the absence of classic clinical symptoms. Few cases of cystic pheochromocytomas have been reported in the literature. We present a case of a huge cystic pheochromocytoma in 70-year-old men who presented with a large retroperitoneal cystic mass and discuss difficulties of diagnostic and treatment.
Irreducible inflamed inguinal hernia with infected gangrenous omentum after laparoscopic appendectomy: a case report
Authors: Awed Andro Adel , Hasoon Haider Ali , Meanji Farid Ahmed , Duhmaj Mostafa Bader , Alamri Khalid Saeed
Published: April 2021

We reported a rare complication of laparoscopic appendectomy in a 19-year-old patient, who was admitted with acute appendicitis and had no history of inguinal hernia. He underwent laparoscopic appendectomy for suppurative appendicitis. Eight days later, he presented with irreducible incarcerated right inguinal hernia. A non-manifested congenital inguinal hernial sac has been symptomized after laparoscopic gas inflation inside the peritoneal cavity, which resulted in widening of the internal inguinal ring and protrusion of the omentum. Besides that, the omental content became inflamed and gangrenous as a consequence of the suppurative appendicitis and the presence of purulent fluid in the pelvis. Therefore, there were two complications that occurred simultaneously after laparoscopic appendectomy: a manifested right inguinal hernia and incarceration and gangrene of its contents. To our knowledge, this is the first reported case of irreducible inflamed inguinal hernia manifested for the first time after laparoscopic appendectomy.
Psittacosis in a traveller
Authors: Veletzky Luzia , Huebl Lena , Schulze zur Wiesch Julian , Schmiedel Stefan
Published: April 2021

A 48-year-old male was admitted with severe community-acquired pneumonia after a family visit to turkey. Upon specific questioning he reported having close contact to a tame budgerigar. Sputum PCR for Chlamydia psittaci turned positive. After treatment adaptation to doxycycline he quickly improved. Detailed anamnesis is paramount for establishing correct diagnosis.
On White Theology … and other Lies: Redemptive Communal Narrative in Toni Morrison’s Beloved
Authors: Allen John J.
Published: April 2021

Toni Morrison’s Beloved can be read as a decidedly theological work, particularly in its expression of redemptive communal unity through narrative re-telling. Morrison’s imagined community in Beloved moves from fragmented isolation to liberative solidarity with each other, dramatically exemplifying a postcolonial theological vision, which draws from African traditional cultures. Although often rejected by some theological interpreters as ‘pop-gnostic’, Toni Morrison’s Beloved rejects a theological worldview of coloniality and offers instead a hybridised approach to theological meaning. In dispelling the racial ‘othering’ that frequently occurs in both literature and theology, Morrison crafts a theological narrative that retells the sinful past in the hope of transcending guilt for the sake of a harmonious future. Thus, the theological insight of Beloved is found in a syncretic cosmology that does not perpetuate colonial ontological categories but forges a communal narrative that is non-possessive and open to a future free from the shackles of the past. Morrison’s Beloved equips the theologian with pertinent questions, ones that wrestle with the presence of God within a suffering and oppressed community; these are timely questions that must be posed to the Christian tradition in order to transcend the lies of white theology.
It is still PCP that can stand for Pneumocystis pneumonia: Appeal for generalized use of only one acronym
Authors: Nevez Gilles , Totet Anne , Matos Olga , Calderon Enrique J , Miller Robert F , Le Gal Solène
Published: April 2021

Twenty-years ago, considering the host specificity of Pneumocystis species, the human-derived Pneumocystis, Pneumocystis carinii formae specialis hominis, was renamed Pneumocystis jirovecii. Pneumocystis carinii formae specialis carinii was finally renamed Pneumocystis carinii and kept for the species derived from Rattus norvegicus. P. jirovecii is now widely used by most authors. The PCP acronym that initially referred to “Pneumocystis cariniipneumonia” was contemporaneously redefined to stand for Pneumocystispneumonia in order to avoid changing the acronym of the name of the disease that clinicians have used for several decades. Using analysis of multidata bases on PubMed, we have noted a recent acceleration in the use of PJP for Pneumocystis jiroveciipneumonia, which may be grammatically correct but not in accordance with retaining PCP, which was proposed in the early 2000s. Through this reminder, in order to standardize the literature on P. jirovecii, we plead for the use of only one acronym, PCP.

Lay Summary

Through this reminder on Pneumocystis nomenclature, we plead for the use of only one acronym, PCP, the retention of which was proposed in the early 2000s, and which currently stands for Pneumocystispneumonia.
Black hole mass measurement using ALMA observations of [CI] and CO emissions in the Seyfert 1 galaxy NGC 7469
Authors: Nguyen Dieu D , Izumi Takuma , Thater Sabine , Imanishi Masatoshi , Kawamuro Taiki , Baba Shunsuke , Nakano Suzuka , Turner Jean L , Kohno Kotaro , Matsushita Satoki , Martín Sergio , Meier David S , Nguyen Phuong M , Nguyen Lam T
Published: April 2021

We present a supermassive black hole (SMBH) mass measurement in the Seyfert 1 galaxy NGC 7469 using Atacama Large Millimeter/submillimeter Array (ALMA) observations of the atomic-[CI](1–0) and molecular-12CO(1–0) emission lines at the spatial resolution of ≈0${_{.}^{\prime\prime}}$3 (or ≈100 pc). These emissions reveal that NGC 7469 hosts a circumnuclear gas disc (CND) with a ring-like structure and a two-arm/bi-symmetric spiral pattern within it, surrounded by a starbursting ring. The CND has a relatively low σgas/V ≈ 0.35 (r ≲ 0${_{.}^{\prime\prime}}$5) and ≈0.19 (r > 0${_{.}^{\prime\prime}}$5), suggesting that the gas is dynamically settled and suitable for dynamically deriving the mass of its central source. As is expected from X-ray dominated region (XDR) effects that dramatically increase an atomic carbon abundance by dissociating CO molecules, we suggest that the atomic [CI](1–0) emission is a better probe of SMBH masses than CO emission in active galactic nuclei (AGNs). Our dynamical model using the [CI](1–0) kinematics yields a $M_{\rm BH}=1.78^{+2.69}_{-1.10}\times 10^7$ M⊙ and $M/L_{\rm F547M}=2.25^{+0.40}_{-0.43}$ (M⊙/L⊙). The model using the 12CO(1–0) kinematics also gives a consistent MBH with a larger uncertainty, up to an order of magnitude, i.e. $M_{\rm BH}=1.60^{+11.52}_{-1.45}\times 10^7$ M⊙. This newly dynamical MBH is ≈2 times higher than the mass determined from the reverberation mapped (RM) method using emissions arising in the unresolved broad-line region (BLR). Given this new MBH, we are able to constrain the specific RM dimensionless scaling factor of $f=7.2^{+4.2}_{-3.4}$ for the AGN BLR in NGC 7469. The gas within the unresolved BLR thus has a Keplerian virial velocity component and the inclination of $i\approx {11.0^\circ }_{-2.5}^{+2.2}$, confirming its face-on orientation in a Seyfert 1 AGN by assuming a geometrically thin BLR model.
Magnetic field and activity phenomena of the K2 dwarf V471 Tau
Authors: Zaire B , Donati J-F , Klein B
Published: April 2021

We analyse spectropolarimetric data of the pre-cataclysmic variable binary system V471 Tau obtained with ESPaDOnS at the Canada–France–Hawaii Telescope in two observational campaigns (in 2004 November/December and 2005 December). Using Zeeman–Doppler imaging, we reconstruct the distribution of brightness map and large-scale magnetic field of the K2 dwarf at both epochs, as well as the amount of differential rotation by which surface maps are sheared. We detect significant fluctuations in the surface shear between the two campaigns. It goes from about twice the solar differential rotation rate to less than the solar value in a 1-yr interval. We conclude that the differential rotation fluctuations obtained for the K2 dwarf resemble those detected on the single-star analogue AB Dor, although even larger amplitudes of variation are seen in the K2 dwarf of V471 Tau. Finally, we show that the differential rotation results obtained in this work do not favour an Applegate mechanism operating in the V471 Tau system, at least in its standard form, but leave room for explaining the observed orbital period fluctuations with exotic forms of similar phenomena based on dynamo processes operating within the convective zone of the K2 star.
Ly α as a tracer of cosmic reionization in the SPHINX radiation-hydrodynamics cosmological simulation
Authors: Garel Thibault , Blaizot Jérémy , Rosdahl Joakim , Michel-Dansac Léo , Haehnelt Martin G , Katz Harley , Kimm Taysun , Verhamme Anne
Published: April 2021

The Ly α emission line is one of the most promising probes of cosmic reionization but isolating the signature of a change in the ionization state of the intergalactic medium (IGM) is challenging because of intrinsic evolution and internal radiation transfer effects. We present the first study of the evolution of Ly α emitters (LAE) during the epoch of reionization based on a full radiation-hydrodynamics cosmological simulation that is able to capture both the large-scale process of reionization and the small-scale properties of galaxies. We predict the Ly α emission of galaxies in the 103 cMpc3sphinx simulation at 6 ≤ z ≤ 9 by computing the full Ly α radiation transfer from interstellar medium (ISM) to IGM scales. sphinx is able to reproduce many observational constraints such as the UV/Ly α luminosity functions and stellar mass functions at z ≳ 6 for the dynamical range probed by our simulation (M1500 ≳ −18, LLy α ≲ 1042 erg s−1, M⋆ ≲ 109 M⊙). As intrinsic Ly α emission and internal Ly α escape fractions barely evolve from z = 6–9, the observed suppression of Ly α luminosities with increasing redshift is fully attributed to IGM absorption. For most observable galaxies (M1500 ≲ −16), the Ly α line profiles are slightly shifted to the red due to internal radiative transfer effects that mitigates the effect of IGM absorption. Overall, the enhanced Ly α suppression during reionization traces the IGM neutral fraction $x_{{\rm H\, {i}}}$ well, but the predicted amplitude of this reduction is a strong function of the Ly α peak shift, which is set at ISM/circumgalactic medium scales. We find that a large number of LAEs could be detectable in very deep surveys during reionization when $x_{{\rm H\, {i}}}$ is still $\approx 50{{\ \rm per\ cent}}$.
Solution structure(s) of trinucleosomes from contrast variation SAXS
Authors: Mauney Alexander W , Muthurajan Uma M , Luger Karolin , Pollack Lois
Published: April 2021

Nucleosomes in all eukaryotic cells are organized into higher order structures that facilitate genome compaction. Visualizing these organized structures is an important step in understanding how genomic DNA is efficiently stored yet remains accessible to information-processing machinery. Arrays of linked nucleosomes serve as useful models for understanding how the properties of both DNA and protein partners affect their arrangement. A number of important questions are also associated with understanding how the spacings between nucleosomes are affected by the histone proteins, chromatin remodelers, or other chromatin-associated protein partners. Contrast variation small angle X-ray scattering (CVSAXS) reports the DNA conformation within protein-DNA complexes and here is applied to measure the conformation(s) of trinucleosomes in solution, with specific sensitivity to the distance between and relative orientation of linked nucleosomes. These data are interpreted in conjunction with DNA models that account for its sequence dependent mechanical properties, and Monte-Carlo techniques that generate realistic structures for comparison with measured scattering profiles. In solution, trinucleosomes segregate into two dominant populations, with the flanking nucleosomes stacked or nearly equilaterally separated, e.g. with roughly equal distance between all pairs of nucleosomes. These populations are consistent with previously observed magnesium-dependent structures of trinucleosomes with shorter linkers.
miRTargetLink 2.0—interactive miRNA target gene and target pathway networks
Authors: Kern Fabian , Aparicio-Puerta Ernesto , Li Yongping , Fehlmann Tobias , Kehl Tim , Wagner Viktoria , Ray Kamalika , Ludwig Nicole , Lenhof Hans-Peter , Meese Eckart , Keller Andreas
Published: April 2021

Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.
Revealed preference analysis and bounded rationality
Authors: Tipoe Eileen , Adams Abi , Crawford Ian
Published: April 2021

The principle of revealed preference is the backbone of structural empirical work on consumer demand. It focuses on what we can learn about the processes by which economic agents make decisions, using observed choices and minimal auxiliary assumptions. Classical revealed preference methods assume that choices and preferences are stable and consistent, but many studies have found violations of these assumptions both in consumer data and experimental settings. Recent research effort extends far beyond the axiomatic characterization of neoclassical choice models. New behavioural theories explain these violations in a theoretically founded way, considering data consistency and preference recoverability for a wide class of behavioural models. This article reviews some of the themes emerging from the recent literature.
Genetic data and niche differences suggest that disjunct populations ofDiglossa brunneiventrisare not sister lineages
Authors: Gutiérrez-Zuluaga Ana M , González-Quevedo Catalina , Oswald Jessica A , Terrill Ryan S , Pérez-Emán Jorge L , Parra Juan L
Published: April 2021

Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here, we describe patterns of geographic differentiation of 2 disjunct populations of Diglossa brunneiventris separated by ~1,000 km along the Andes. Diglossa brunneiventris vuilleumieri is isolated in northern Colombia, while Diglossa brunneiventris brunneiventris has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the 2 D. brunneiventris subspecies to evaluate whether they form a monophyletic clade, while including the other 3 species within the carbonaria complex (D. gloriosa, D. humeralis, and D. carbonaria). We also constructed ecological niche models for each D. brunneiventris subspecies to compare their climatic niches. We found that when using all available molecular data, the 2 D. brunneiventris subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.
Hidden Spaces of Empire: Italian Colonists in Nineteenth-Century Peru
Authors: Riall Lucy
Published: April 2021

Among the clichés in modern European history, one of the most common is of Italy as ‘the least of the Great Powers’, unable to punch above its weight in the international arena and classed as a ‘latecomer’ to imperial conquest. In this article, I suggest instead that historians have been looking in the wrong place, and in the wrong period, for evidence of Italian ambition. By concentrating on territorial acquisitions in Africa, they are assessing only a small, relatively unproductive and arguably atypical slice of Italy’s global presence. I argue that even before national unification, and long before acquiring a formal Empire, Italy built a global influence structured by the activities of overseas migrants. Yet, despite the recent ‘turn’ to global history and the stress on diversity in colonial experience, the chronology and geography of the European nation-state still shape our understanding of nineteenth-century Empire. Looking at the hugely successful Italian colony in Peru, at both its commercial and scientific interests and at a violent attempt to establish a settler colony in Chanchamayo, in the Peruvian Amazon, I argue that this Italian world was driven not a nation state but relied instead on a common culture, a culture that was created by a capacity for local assimilation, by Catholic notions of civilisation and by ideas of white racial superiority. Modern imperialism was shaped as much by ‘lesser’ powers, often before – or without – the nation-state, and in continuity with the practices of the early-modern period. Moreover, mundane migrants could be the most successful empire-builders. I conclude with a call to take note of the full and diverse range of nineteenth-century colonial activities, and not to assume the primacy of formal Empires in the period of ‘High Imperialism.’
Exploring the Contribution and Relationship to Policing and Community Safety of Volunteer Street Patrols
Authors: Westall Adam
Published: April 2021

The pluralized policing landscape now widely involves volunteers and the voluntary sector. Volunteer street patrols (VSPs) are individuals who walk the streets of cities and towns at night. Their actions include helping those in need through acts of care, compassion, and prevention. Numerous implications exist for the volunteers who participate in this form of voluntary action, including the level to which volunteers contribute and intervene, the functions they perform within contemporary policing, and the challenges of developing and maintaining relationships with the police and other emergency services. This article argues that VSPs offer a unique and welcomed source of support to the police, providing functions the police are unable to perform. The relationship provides validity, accountability, and opportunity for the volunteers. Over reliance, increased responsibilization and challenges for volunteers delivering policing services highlight tensions in the relationship, which in turn create opportunities to develop meaningful partnerships.
Averting a public health crisis in England’s coastal communities: a call for public health research and policy
Authors: Asthana Sheena , Gibson Alex
Published: April 2021

Coastal communities have received little attention in the public health literature, perhaps because our mental maps tend to associate socio-economic deprivation and health inequalities with inner cities. Mapping a range of key health indicators at small area level, this paper reveals a distinct core-periphery pattern in disease prevalence, with coastal communities experiencing a high burden of ill health across almost all conditions included in the Quality and Outcomes Framework dataset. Other sources suggest poor outcomes for children and young people living in coastal areas. Low rates of participation in higher education contrast with high rates of hospitalisation for self-harm, alcohol and substance use. Reflecting a shift in the distribution of children living in poverty since the 1990s, this may be an early indicator of a future public health crisis in these communities. Exploring reasons for the health challenges facing the periphery, this perspective piece calls for more public health research that can accommodate the complex and interlinked problems facing coastal communities and a more concerted effort to align public health with economic, education, local government and transport policies at the national level.
The Effects of a Targeted Financial Constraint on the Housing Market
Authors: Han Lu , Lutz Chandler , Sand Benjamin , Stacey Derek
Published: April 2021

We study how financial constraints affect the housing market by exploiting a regulatory change that increases the down payment requirement for homes selling for $\$$1M or more. Using Toronto data, we find that the policy causes excess bunching of homes listed at $\$$1M and heightened bidding intensity for these homes, but only a muted response in sales. While difficult to reconcile in a frictionless market, these findings are consistent with the implications derived from an equilibrium search model with auctions and financial constraints. Our analysis points to the importance of designing macroprudential policies that recognize the strategic responses of market participants.
Selecting Directors Using Machine Learning
Authors: Erel Isil , Stern Léa H , Tan Chenhao , Weisbach Michael S
Published: April 2021

Can algorithms assist firms in their decisions on nominating corporate directors? Directors predicted by algorithms to perform poorly indeed do perform poorly compared to a realistic pool of candidates in out-of-sample tests. Predictably bad directors are more likely to be male, accumulate more directorships, and have larger networks than the directors the algorithm would recommend in their place. Companies with weaker governance structures are more likely to nominate them. Our results suggest that machine learning holds promise for understanding the process by which governance structures are chosen and has potential to help real-world firms improve their governance.