bluuebunny/crossref_metadata_2025_split huggingface dataset:
OSIRIS: A Minimum Data Set for Data Sharing and Interoperability in Oncology
Authors: Guérin Julien , Laizet Yec'han , Le Texier Vincent , Chanas Laetitia , Rance Bastien , Koeppel Florence , Lion François , Gourgou Sophie , Martin Anne-Laure , Tejeda Manuel , Toulmonde Maud , Cox Stéphanie , Hess Elisabeth , Rousseau-Tsangaris Marina , Jouhet Vianney , Saintigny Pierre 
Published: March 2021

PURPOSE Many institutions throughout the world have launched precision medicine initiatives in oncology, and a large amount of clinical and genomic data is being produced. Although there have been attempts at data sharing with the community, initiatives are still limited. In this context, a French task force composed of Integrated Cancer Research Sites (SIRICs), comprehensive cancer centers from the Unicancer network (one of Europe's largest cancer research organization), and university hospitals launched an initiative to improve and accelerate retrospective and prospective clinical and genomic data sharing in oncology. MATERIALS AND METHODS For 5 years, the OSIRIS group has worked on structuring data and identifying technical solutions for collecting and sharing them. The group used a multidisciplinary approach that included weekly scientific and technical meetings over several months to foster a national consensus on a minimal data set. RESULTS The resulting OSIRIS set and event-based data model, which is able to capture the disease course, was built with 67 clinical and 65 omics items. The group made it compatible with the HL7 Fast Healthcare Interoperability Resources (FHIR) format to maximize interoperability. The OSIRIS set was reviewed, approved by a National Plan Strategic Committee, and freely released to the community. A proof-of-concept study was carried out to put the OSIRIS set and Common Data Model into practice using a cohort of 300 patients. CONCLUSION Using a national and bottom-up approach, the OSIRIS group has defined a model including a minimal set of clinical and genomic data that can be used to accelerate data sharing produced in oncology. The model relies on clear and formally defined terminologies and, as such, may also benefit the larger international community.
Igf signaling couples retina growth with body growth by modulating progenitor cell division
Authors: Becker Clara , Lust Katharina , Wittbrodt Joachim 
Published: March 2021

ABSTRACT
How the body and organs balance their relative growth is of key importance for coordinating size and function. This is of particular relevance in organisms, which continue to grow over their entire life span. We addressed this issue in the neuroretina of medaka fish (Oryzias latipes), a well-studied system with which to address vertebrate organ growth. We reveal that a central growth regulator, Igf1 receptor (Igf1r), is necessary and sufficient for proliferation control in the postembryonic retinal stem cell niche: the ciliary marginal zone (CMZ). Targeted activation of Igf1r signaling in the CMZ uncouples neuroretina growth from body size control, and we demonstrate that Igf1r operates on progenitor cells, stimulating their proliferation. Activation of Igf1r signaling increases retinal size while preserving its structural integrity, revealing a modular organization in which progenitor differentiation and neurogenesis are self-organized and highly regulated. Our findings position Igf signaling as a key module for controlling retinal size and composition, with important evolutionary implications.
Identification of a novel Bax–Cdk1 signalling complex that links activation of the mitotic checkpoint to apoptosis
Authors: Darweesh Omeed , Al-Shehri Eman , Falquez Hugo , Lauterwasser Joachim , Edlich Frank , Patel Rajnikant 
Published: March 2021

ABSTRACT
In eukaryotes, entry into and exit from mitosis is regulated, respectively, by the transient activation and inactivation of Cdk1. Taxol, an anti-microtubule anti-cancer drug, prevents microtubule–kinetochore attachments to induce spindle assembly checkpoint (SAC; also known as the mitotic checkpoint)-activated mitotic arrest. SAC activation causes mitotic arrest by chronically activating Cdk1. One consequence of prolonged Cdk1 activation is cell death. However, the cytoplasmic signal(s) that link SAC activation to the initiation of cell death remain unknown. We show here that activated Cdk1 forms a complex with the pro-apoptotic proteins Bax and Bak (also known as BAK1) during SAC-induced apoptosis. Bax- and Bak-mediated delivery of activated Cdk1 to the mitochondrion is essential for the phosphorylation of the anti-apoptotic proteins Bcl-2 and Bcl-xL (encoded by BCL2L1) and the induction of cell death. The interactions between a key cell cycle control protein and key pro-apoptotic proteins identify the Cdk1–Bax and Cdk1–Bak complexes as the long-sought-after cytoplasmic signal that couples SAC activation to the induction of apoptotic cell death.
Rab5 regulates macropinocytosis by recruiting the inositol 5-phosphatases OCRL and Inpp5b that hydrolyse PtdIns(4,5)P2
Authors: Maxson Michelle E. , Sarantis Helen , Volchuk Allen , Brumell John H. , Grinstein Sergio 
Published: March 2021

ABSTRACT
Rab5 is required for macropinosome formation, but its site and mode of action remain unknown. We report that Rab5 acts at the plasma membrane, downstream of ruffling, to promote macropinosome sealing and scission. Dominant-negative Rab5, which obliterates macropinocytosis, had no effect on the development of membrane ruffles. However, Rab5-containing vesicles were recruited to circular membrane ruffles, and soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-dependent endomembrane fusion was necessary for the completion of macropinocytosis. This fusion event coincided with the disappearance of PtdIns(4,5)P2 that accompanies macropinosome closure. Counteracting the depletion of PtdIns(4,5)P2 by expression of phosphatidylinositol-4-phosphate 5-kinase impaired macropinosome formation. Importantly, we found that the removal of PtdIns(4,5)P2 is dependent on Rab5, through the Rab5-mediated recruitment of the inositol 5-phosphatases OCRL and Inpp5b, via APPL1. Knockdown of OCRL and Inpp5b, or APPL1, prevented macropinosome closure without affecting ruffling. We therefore propose that Rab5 is essential for the clearance of PtdIns(4,5)P2 needed to complete the scission of macropinosomes or to prevent their back-fusion with the plasmalemma.
A robust and flexible CRISPR/Cas9-based system for neutrophil-specific gene inactivation in zebrafish
Authors: Wang Yueyang , Hsu Alan Y. , Walton Eric M. , Park Sung Jun , Syahirah Ramizah , Wang Tianqi , Zhou Wenqing , Ding Chang , Lemke Abby Pei , Zhang GuangJun , Tobin David M. , Deng Qing 
Published: March 2021

ABSTRACT
CRISPR/Cas9-based tissue-specific knockout techniques are essential for probing the functions of genes in embryonic development and disease using zebrafish. However, the lack of capacity to perform gene-specific rescue or live imaging in the tissue-specific knockout background has limited the utility of this approach. Here, we report a robust and flexible gateway system for tissue-specific gene inactivation in neutrophils. Using a transgenic fish line with neutrophil-restricted expression of Cas9 and ubiquitous expression of single guide (sg)RNAs targeting rac2, specific disruption of the rac2 gene in neutrophils is achieved. Transient expression of sgRNAs targeting rac2 or cdk2 in the neutrophil-restricted Cas9 line also results in significantly decreased cell motility. Re-expressing sgRNA-resistant rac2 or cdk2 genes restores neutrophil motility in the corresponding knockout background. Moreover, active Rac and force-bearing F-actins localize to both the cell front and the contracting tail during neutrophil interstitial migration in an oscillating fashion that is disrupted when rac2 is knocked out. Together, our work provides a potent tool that can be used to advance the utility of zebrafish in identifying and characterizing gene functions in a tissue-specific manner.
Factors influencing non-adherence to opioids in cancer patients: a mixed-methods cross-sectional study
Authors: Seangrung Rattaphol , Ahuja Mallika , Pasutharnchat Koravee , Mahawan Rungwipha 
Published: March 2021

Background: Strong opioids are mainly utilized to attenuate pain in cancer patients. Adherence to analgesic drugs significantly promotes adequate pain management and improves quality of life. We aimed to identify the factors influencing non-adherence to strong opioids in cancer patients. Methods: A descriptive, cross-sectional, two-phased, mixed methods design was conducted prospectively to evaluate a cohort of 101 cancer patients who are currently prescribed strong opioids from a pain clinic in Thailand between January and March 2018. Participants were asked to complete a questionnaire that included the following sections: general characteristics; the Medication Taking Behavior in Thai (MTB-Thai) for assessing adherence to medications; and factors influencing nonadherence, which were analyzed using multivariate logistic regression. In addition, face-to-face in depth interviews were conducted with patients showing non-adherence to strong opioids (MTB-Thai score ≤21) and analyzed using thematic content analysis. Results: Of 101 cancer pain patients that completed the questionnaire, 39.6% showed non-adherence to strong opioids. Illness understanding (P=0.047) and the use of more than three types of pain medication (P=0.032) were significant factors influencing non-adherence. Qualitative analysis indicated that fear of long-term outcomes, opioid side effects, ineffective pain control, attempts to make the regimen more acceptable, poor understanding, and non-acceptance of disease related to non-adherence. Conclusion: Non-adherence to opioids for cancer patients is a common problem. Awareness of patient factors, medication-related factors, and illness-related factors will provide the knowledge and adequate advice that may enhance adherence to medications.
Programmable, direct space-to-time picosecond resolution pulse shaper with nanosecond record
Authors: Mittelberger D. E. , Muir R. , Perlmutter D. , Heebner J. 
Published: March 2021

We demonstrate a novel, to the best of our knowledge, extension of optical arbitrary waveform generation capable of picosecond resolution over nanosecond duration. The method, called space–time induced linearly encoded transcription for temporal optimization, is based on direct space-to-time pulse shaping and is extended here to single-mode output with a programmable temporal profile. We develop the theory of operation and discuss ultimate limits on resolution, record length, and efficiency. We report on the results of an experimental demonstration showing

∼

1

p
s

resolution over 600 ps.
Second and third harmonic conversion of a kilowatt average power, 100-J-level diode pumped Yb:YAG laser in large aperture LBO
Authors: Phillips Jonathan P. , Banerjee Saumyabrata , Mason Paul , Smith Jodie , Spear Jacob , De Vido Mariastefania , Ertel Klaus , Butcher Thomas , Quinn Gary , Clarke Danielle , Edwards Chris , Hernandez-Gomez Cristina , Collier John 
Published: March 2021

We report on the successful demonstration of second and third harmonic
conversion of a high pulse energy, high average power 1030 nm diode
pumped Yb-doped yttrium aluminum garnet (Yb:YAG) nanosecond pulsed
laser in a large aperture lithium triborate (LBO) crystal. We
demonstrated generation of 59.7 J at 10 Hz (597 W) at 515 nm (second
harmonic) and of 65.0 J at 1 Hz (65 W) at 343 nm (third harmonic),
with efficiencies of 66% and 68%, respectively. These results, to the
best of our knowledge, represent the highest energy and power reported
for frequency conversion to green and UV-A wavelengths.
Opportunistic feeding behaviour and Leishmania infantum detection in Phlebotomus perniciosus females collected in the human leishmaniasis focus of Madrid, Spain (2012–2018)
Authors: González Estela , Molina Ricardo , Iriso Andrés , Ruiz Sonia , Aldea Irene , Tello Ana , Fernández Daniel , Jiménez Maribel 
Published: March 2021

Background
An outbreak of human leishmaniasis due to Leishmania infantum has been registered in an urban area of southwestern Madrid, Spain, since 2010. Entomological surveys carried out in the municipalities of Fuenlabrada, Leganés, Getafe and Humanes de Madrid showed that Phlebotomus perniciosus is the only potential vector. In this work, an intensive molecular surveillance was performed in P. perniciosus females captured in the region between 2012 and 2018.

Methodology/Principal findings
A total of 1805 P. perniciosus females were analyzed for Leishmania infection, and 1189 of them also for bloodmeal identification. Eleven different species of vertebrate were detected by amplification and subsequent sequencing of the 359 bp cytb fragment. The most prevalent blood source identified was hare (n = 553, 46.51%), followed by rabbit (n = 262, 21.95%). Less frequent were cat (n = 45, 3.80%), human (n = 34, 2.90%), pig (n = 14, 1.20%), horse (n = 11, 0.93%), sheep (n = 3, 0.25%), rhea (n = 3, 0.25%), partridge (n = 1, 0.09%) and chicken (n = 1, 0.09%). The distribution of the blood meal sources varied between the different locations. Regarding L. infantum detection, PCR amplification of a fragment of kDNA, cpb gene and ITS1 region showed 162 positive specimens (8.97%). The highest infection rate was found in the municipality of Leganés (15.17%).

Conclusions
The results of this molecular survey in P. perniciosus, the only leishmaniasis vector in the outbreak occurred in southwestern Madrid region, showed its opportunistic blood-feeding behaviour, high infection rates and the differences between the different points. This study was an essential part of the intensive surveillance plan in the area and the results obtained have supported the implementation of control measures in the outbreak.
Outcomes of COVID-19 patients with comorbidities in southwest Nigeria
Authors: Osibogun Akin , Balogun Mobolanle , Abayomi Akin , Idris Jide , Kuyinu Yetunde , Odukoya Oluwakemi , Wright Ololade , Adeseun Remi , Mutiu Bamidele , Saka Babatunde , Osa Nike , Lajide Dayo , Abdus-Salam Ismael , Osikomaiya Bodunrin , Onasanya Oluwatosin , Adebayo Bisola , Oshodi Yewande , Adesola Sunday , Adejumo Olu , Erinoso Olufemi , Abdur-Razzaq Hussein , Bowale Abimbola , Akinroye Kingsley 
Published: March 2021

Background
Data on the comorbidities that result in negative outcomes for people with COVID-19 are currently scarce for African populations. This study identifies comorbidities that predict death among a large sample of COVID-19 patients from Nigeria.

Methods
This was a retrospective analysis of medical records for 2184 laboratory confirmed cases of COVID-19 in Lagos, southwest Nigeria. Extracted data included age, sex, severity of condition at presentation and self-reported comorbidities. The outcomes of interest were death or discharge from facility.

Results
Most of the cases were male (65.8%) and the median age was 43 years (IQR: 33–55). Four hundred and ninety-two patients (22.5%) had at least one comorbidity and the most common amongst them were hypertension (74.2%) and diabetes (30.3%). The mortality rate was 3.3% and a significantly higher proportion of patients with comorbidities died compared to those with none. The comorbidities that predicted death were hypertension (OR: 2.21, 95%CI: 1.22–4.01), diabetes (OR: 3.69, 95% CI: 1.99–6.85), renal disease (OR: 12.53, 95%CI: 1.97–79.56), cancer (OR: 14.12, 95% CI: 2.03–98.19) and HIV (OR: 1.77–84.15].

Conclusion
Comorbidities are prevalent and the associated risk of death is high among COVID-19 patients in Lagos, Nigeria. Public enlightenment, early identification and targeted care for COVID-19 cases with comorbidities are recommended as the pandemic evolves.
Changes in the prevalence of self-reported sexually transmitted bacterial infections from 2010 and 2017 in two large European samples of men having sex with men–is it time to re-evaluate STI-screening as a control strategy?
Authors: Marcus Ulrich , Mirandola Massimo , Schink Susanne B. , Gios Lorenzo , Schmidt Axel J. 
Published: March 2021

Background/ObjectivesMany European countries reported increased numbers of syphilis, gonorrhoea and chlamydia diagnoses among men who have sex with men (MSM) in recent years. Behaviour changes and increased testing are thought to drive these increases.MethodsIn 2010 and 2017, two large online surveys for MSM in Europe (EMIS-2010, EMIS-2017) collected self-reported data on STI diagnoses in the previous 12 months, diagnostic procedures, STI symptoms when testing, number of sexual partners, and sexual behaviours such as condom use during the last intercourse with a non-steady partner in 46 European countries. Multivariate regression models were used to analyse factors associated with diagnoses of syphilis, gonorrhoea/chlamydia, and respective diagnoses classified as symptomatic and asymptomatic. If applicable, they included country-level screening rates.ResultsQuestions on STI diagnoses and sexual behaviours were answered by 156,018 (2010) and 125,837 (2017) participants. Between 2010 and 2017, overall diagnoses with gonorrhoea/chlamydia and syphilis increased by 76% and 83% across countries. Increases were more pronounced for asymptomatic compared to symptomatic infections. The proportion of respondents screened and the frequency of screening grew considerably. Condomless anal intercourse with the last non-steady partner rose by 62%; self-reported partner numbers grew. Increased syphilis diagnoses were largely explained by behavioural changes (including more frequent screening). Gonorrhoea/chlamydia increases were mainly explained by more screening and a change in testing performance. A country variable representing the proportion of men screened for asymptomatic infection was positively associated with reporting symptomatic gonorrhoea/chlamydia, but not syphilis.Discussion/ConclusionThe positive association of country-level screening rates with the proportion of symptomatic infections with gonorrhoea/chlamydia may indicate a paradoxical effect of screening on incidence of symptomatic infections. Treatment of asymptomatic men might render them more susceptible to new infections, while spontaneous clearance may result in reduced susceptibility. Before expanding screening programmes, evidence of the effects of screening and treatment is warranted.
Accuracy of abbreviated protocols for unattended automated office blood pressure measurements, a retrospective study
Authors: Vischer Annina S. , Hug Rebecca , Socrates Thenral , Meienberg Andrea , Mayr Michael , Burkard Thilo 
Published: March 2021

Background
Blood pressure measurement (BPM) is one of the most often performed procedures in clinical practice, but especially office BPM is prone to errors. Unattended automated office BPM (AOBPM) is somewhat standardised and observer-independent, but time and space consuming. We aimed to assess whether an AOBPM protocol can be abbreviated without losing accuracy.

Design
In our retrospective single centre study, we used all AOBPM (AOBPM protocol of the SPRINT study), collected over 14 months. Three sequential BPM (after 5 minutes of rest, spaced 2 minutes) were automatically recorded with the patient alone in a quiet room resulting in three systolic and diastolic values. We compared the mean of all three (RefProt) with the mean of the first two (ShortProtA) and the single first BPM (ShortProtB).

Results
We analysed 413 AOBPM sets from 210 patients. Mean age was 52±16 years. Mean values for RefProt were 128.3/81.3 mmHg, for ShortProtA 128.4/81.4 mmHg, for ShortProtB 128.8/81.4 mmHg. Mean difference and limits of agreement for RefProt vs. ShortProtA and ShortProtB were -0.1±4.2/-0.1±2.8 mmHg and -0.5±8.1/-0.1±5.3 mmHg, respectively. With ShortProtA, 83% of systolic and 92% of diastolic measurements were within 2 mmHg from RefProt (67/82% for ShortProtB). ShortProtA or ShortProtB led to no significant hypertensive reclassifications in comparison to RefProt (p-values 0.774/1.000/1.000/0.556).

Conclusion
Based on our results differences between the RefProt and ShortProtA are minimal and within acceptable limits of agreement. Therefore, the automated procedure may be shorted from 3 to 2 measurements, but a single measurement is insufficient.
Plotinus on Care of Self and Soul
Authors: Regnier Daniel 
Published: March 2021

Plotinus’ philosophical project includes an important Socratic element. Plotinus is namely interested in both self-knowledge and care of soul and self. In this study I examine how through his interpretation of three passages from Plato (Timaeus 35 a, Phaedrus 246 band Theatetus 176 a-b), Plotinus develops an account of the role of care in his ethics. Care in Plotinus’ ethical thought takes three forms. First of all, care is involved in maintaining the unity of the embodied self. Secondly, situated in a providential universe, our souls – as sisters to the world soul - take part in the providential order by caring for ‘lower’ realities. Finally, Plotinus develops an ethics of going beyond virtue, a process which involves care for the higher, potentially divine, self.
The use of shells in the architecture of the concert halls
Authors: Ermakova Evgenia , Rynkovskaya Marina 
Published: March 2021

Abstract
This paper deals with the use of the shells in the architecture of concert halls through research on the historical development of the concert building’s space. These elements are widely applied in civil engineering and architecture due to the good operational qualities, very rich spectrum of forms, the simplicity of production and its technical efficiency. The article considers two types of shells: conoid and truncated cone to choose the most optimal form for covering the concert hall.
The ℓ-modular representation of reductive groups over finite local rings of length two
Authors: Monteiro Nariel 
Published: March 2021

Abstract
Let

O
2

\mathcal{O}_{2}

and

O
2
′

\mathcal{O}^{\prime}_{2}

be two distinct finite local rings of length two with residue field of characteristic 𝑝.
Let

G
⁢

(

O
2

)

\mathbb{G}(\mathcal{O}_{2})

and

G
⁢

(

O
2
′

)

\mathbb{G}(\mathcal{O}^{\prime}_{2})

be the groups of points of any reductive group scheme 𝔾 over ℤ such that 𝑝 is very good for

G
×

F
q

\mathbb{G}\times\mathbb{F}_{q}

or

G
=

GL
n

\mathbb{G}=\operatorname{GL}_{n}

.
We prove that there exists an isomorphism of group algebras

K
⁢
G
⁢

(

O
2

)

≅

K
⁢
G
⁢

(

O
2
′

)

K\mathbb{G}(\mathcal{O}_{2})\cong K\mathbb{G}(\mathcal{O}^{\prime}_{2})

, where 𝐾 is a sufficiently large field of characteristic different from 𝑝.