bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explainability for deep learning in mammography image quality assessment
Authors: Amanova N , Martin J , Elster C 
Published: June 2022

Abstract
The application of deep learning has recently been proposed for the assessment of image quality in mammography. It was demonstrated in a proof-of-principle study that the proposed approach can be more efficient than currently applied automated conventional methods. However, in contrast to conventional methods, the deep learning approach has a black-box nature and, before it can be recommended for the routine use, it must be understood more thoroughly. For this purpose, we propose and apply a new explainability method: the oriented, modified integrated gradients (OMIG) method. The design of this method is inspired by the integrated gradientsmethod but adapted considerably to the use case at hand. To further enhance this method, an upsampling technique is developed that produces high-resolution explainability maps for the downsampled data used by the deep learning approach. Comparison with established explainability methods demonstrates that the proposed approach yields substantially more expressive and informative results for our specific use case. Application of the proposed explainability approach generally confirms the validity of the considered deep learning-based mammography image quality assessment (IQA) method. Specifically, it is demonstrated that the predicted image quality is based on a meaningful mapping that makes successful use of certain geometric structures of the images. In addition, the novel explainability method helps us to identify the parts of the employed phantom that have the largest impact on the predicted image quality, and to shed some light on cases in which the trained neural networks fail to work as expected. While tailored to assess a specific approach from deep learning for mammography IQA, the proposed explainability method could also become relevant in other, similar deep learning applications based on high-dimensional images.
Almost everywhere convergence of spectral sums for self-adjoint operators
Authors: Chen Peng , Duong Xuan Thinh , Yan Lixin 
Published: June 2022

Let

L
L

be a non-negative self-adjoint operator acting on the space

L
2

(
X
)

L^2(X)

, where

X
X

is a positive measure space. Let

L

=

∫
0

∞

λ
d

E

L

(

λ

)

{ L}=\int _0^{\infty } \lambda dE_{ L}({\lambda })

be the spectral resolution of

L
L

and

S
R

(

L

)
f
=

∫
0
R

d

E

L

(
λ
)
f

S_R({ L})f=\int _0^R dE_{ L}(\lambda ) f

denote the spherical partial sums in terms of the resolution of

L

{ L}

. In this article we give a sufficient condition on

L
L

such that

lim

R
→
∞

S
R

(

L

)
f
(
x
)
=
f
(
x
)
,

a.e.

\begin{equation*} \lim _{R\rightarrow \infty } S_R({ L})f(x) =f(x),\ \ \text {a.e.} \end{equation*}

for any

f
f

such that

log
⁡
(
2
+
L
)
f
∈

L
2

(
X
)

\operatorname {log}(2+L) f\in L^2(X)

. These results are applicable to large classes of operators including Dirichlet operators on smooth bounded domains, the Hermite operator and Schrödinger operators with inverse square potentials.
CircAHNAK upregulates EIF2B5 expression to inhibit the progression of ovarian cancer by modulating the JAK2/STAT3 signaling pathway
Authors: He Si-Li , Zhao Xingping , Yi Shui-Jing 
Published: June 2022

Abstract
Recent studies highlighted non-coding RNAs as potential therapeutic targets in ovarian cancer. We aimed to investigate the roles of circAHNAK in ovarian cancer pathogenesis. Here, RNA immunoprecipitation, dual-luciferase reporter assay and RNA fluorescence in situ hybridization were adopted to determine circAHNAK, miR-28 or EIF2B5 interaction. CCK-8 assay was used to detect cell proliferation. Wound healing and Transwell assays were employed to assess cell migration and invasion, respectively. Flow cytometry was performed to measure cell apoptosis. The roles of circAHNAK on tumor growth in vivo were evaluated using subcutaneous xenograft model. The expression levels of circAHNAK, miR-28, EIF2B5, markers of EMT and JAK2/STAT3 pathway were measured by qRT-PCR, western blotting or immunohistochemistry staining. We reported that circAHNAK was decreased in ovarian cancer tissues. Forced expression of circAHNAK promoted apoptosis and inhibited cell proliferation, migration, invasion, EMT and JAK2/STAT3 signaling pathway. Mechanistically, circAHNAK acted as a miR-28 sponge. CircAHNAK deficiency resulted in the amassing of miR-28, which was elevated in ovarian cancer and promoted cancer cell malignancy. MiR-28 in turn inhibited EIF2B5 expression. Silence of EIF2B5 abolished the anticancer effects of miR-28 inhibitor. CircAHNAK overexpression retarded tumor growth in vivo, along with the decreased miR-28 and increased EIF2B, as well as EMT inhibition. In conclusion, circAHNAK targets miR-28 to upregulate EIF2B5 expression, thus inhibits progression of ovarian cancer by suppressing JAK2/STAT3 signaling pathway.
Minimally invasive mitral valve surgery after failed transcatheter mitral valve repair in an intermediate-risk cohort
Authors: Akansel Serdar , Kofler Markus , Van Praet Karel M , Unbehaun Axel , Sündermann Simon H , Jacobs Stephan , Falk Volkmar , Kempfert Jörg 
Published: June 2022

Abstract

OBJECTIVES
Although clinical experience with transcatheter mitral valve interventions is rapidly increasing, there is still a lack of evidence regarding surgical treatment options for the management of recurrent mitral regurgitation (MR). This study provides guidance for a minimally invasive surgical approach following failed transcatheter mitral valve repair, which is based on the underlying mitral valve (MV) pathology and the type of intervention.

METHODS
A total of 46 patients who underwent minimally invasive MV surgery due to recurrent or residual MR after transcatheter edge-to-edge repair or direct interventional annuloplasty between October 2014 and March 2021 were included.

RESULTS
The median age of the patients was 78 [interquartile range, 71–82] years and the EuroSCORE II was 4.41 [interquartile range, 2.66–6.55]. At the index procedure, edge-to-edge repair had been performed in 45 (97.8%) patients and direct annuloplasty in 1 patient. All patients with functional MR at the index procedure (n = 36) underwent MV replacement. Of the patients with degenerative MR (n = 10), 5 patients were eligible for MV repair after removal of the MitraClip. The 1-year survival following surgical treatment was 81.3% and 75.0% in patients with functional and degenerative MR, respectively. No residual MR greater than mild during follow-up was observed in patients who underwent MV repair.

CONCLUSIONS
Minimally invasive surgery following failed transcatheter mitral valve repair is feasible and safe, with promising midterm survival. The surgical management should be tailored to the underlying valve pathology at the index procedure, the extent of damage of the MV leaflets and the type of previous intervention.
Evidence of reduced academic performance among schoolchildren with helminth infection
Authors: Donkoh Emmanuel T , Berkoh Dorice , Fosu-Gyasi Samuel , Boadu Wina I Ofori , Raji Abdul S , Asamoah Samuel , Otabil Kenneth B , Otoo John E , Yeboah Michael T , Aganbire Benedicta A , Adobasom-Anane Austin G , Adams Simon K , Debrah Oksana ,   Screen and Treat Research Group, Boadu Kwame O , Amelor Dodzi , Obirikorang Christian , Nkrumah Kwame , Dassah Edward T , Afful Enoch , Ansah Barimah 
Published: June 2022

Abstract

Background
Soil-transmitted helminths (STHs) pose a formidable health risk to school-age children in resource-limited settings. Unfortunately, mass deworming campaigns have been derailed since the onset of the coronavirus disease 2019 pandemic. The present study assessed the cross-sectional associations between STHs, nutritional status and academic performance of schoolchildren in the Banda District of Ghana.

Methods
Schoolchildren (5–16 y of age; n=275) were recruited through both school and household visits by community health workers using a multistage cluster sampling technique. In addition to school microscopy, anthropometric records were also taken.

Results
The prevalence of geohelminthiasis was 40.4% (95% confidence interval 34.6 to 46.2). STHs targeted for elimination by the World Health Organization and national programmes were detected among schoolchildren. Children with intestinal parasite infection (53.7 [standard deviation {SD} 11.5]) had lower mean academic scores compared with uninfected children (59.6 [SD 16.9]) (p=0.034). In multiple regression analysis, intestinal parasite infection status and z-scores for weight-for-age showed a collective significant effect on the academic score (F1117=8.169, p&lt;0.001, R2=0.125).

Conclusions
Schoolchildren with STHs had poorer academic performance compared with uninfected children, despite their nutritional status. In addition to school feeding programmes, school-based mass drug administration campaigns may be critical for improving learning outcomes in young schoolchildren.
Synthetic oxepanoprolinamide iboxamycin is active against Listeria monocytogenes despite the intrinsic resistance mediated by VgaL/Lmo0919 ABCF ATPase
Authors: Brodiazhenko Tetiana , Turnbull Kathryn Jane , Wu Kelvin J Y , Takada Hiraku , Tresco Ben I C , Tenson Tanel , Myers Andrew G , Hauryliuk Vasili 
Published: June 2022

Abstract

Background
Listeriosis is a food-borne disease caused by the Gram-positive Bacillota (Firmicute) bacterium Listeria monocytogenes. Clinical L. monocytogenes isolates are often resistant to clinically used lincosamide clindamycin, thus excluding clindamycin as a viable treatment option.

Objectives
We have established newly developed lincosamide iboxamycin as a potential novel antilisterial agent.

Methods
We determined MICs of the lincosamides lincomycin, clindamycin and iboxamycin for L. monocytogenes, Enterococcus faecalis and Bacillus subtilis strains expressing synergetic antibiotic resistance determinants: ABCF ATPases that directly displace antibiotics from the ribosome and Cfr, a 23S rRNA methyltransferase that compromises antibiotic binding. For L. monocytogenes strains, either expressing VgaL/Lmo0919 or lacking the resistance factor, we performed time-kill kinetics and post-antibiotic effect assays.

Results
We show that the synthetic lincosamide iboxamycin is highly active against L. monocytogenes and can overcome the intrinsic lincosamide resistance mediated by VgaL/Lmo0919 ABCF ATPase. While iboxamycin is not bactericidal against L. monocytogenes, it displays a pronounced post-antibiotic effect, which is a valuable pharmacokinetic feature. We demonstrate that VmlR ABCF of B. subtilis grants significant (33-fold increase in MIC) protection from iboxamycin, while LsaA ABCF of E. faecalis grants an 8-fold protective effect. Furthermore, the VmlR-mediated iboxamycin resistance is cooperative with that mediated by the Cfr, resulting in up to a 512-fold increase in MIC.

Conclusions
While iboxamycin is a promising new antilisterial agent, our findings suggest that emergence and spread of ABCF ARE variants capable of defeating next-generation lincosamides in the clinic is possible and should be closely monitored.
Articulation of postsurgical patient discharges: coordinating care transitions from hospital to home
Authors: Abraham Joanna , Kandasamy Madhumitha , Huggins Ashley 
Published: June 2022

Abstract

Background
Cardiac surgery patients are at high risk for readmissions after hospital discharge- few of these readmissions are preventable by mitigating barriers underlying discharge care transitions. An in-depth evaluation of the nuances underpinning the discharge process and the use of tools to support the process, along with insights on patient and clinician experiences, can inform the design of evidence-based strategies to reduce preventable readmissions.

Objective
The study objectives are 3-fold: elucidate perceived factors affecting the postsurgical discharge care transitions of cardiac surgery patients going home; highlight differences among clinician and patient perceptions of the postsurgical discharge experiences, and ascertain the impact of these transitions on patient recovery at home.

Methods
We conducted a prospective multi-stakeholder study using mixed methods, including general observations, patient shadowing, chart reviews, clinician interviews, and follow-up telephone patient and caregiver surveys/interviews. We followed thematic and content analyses.

Findings
Participants included 49 patients, 6 caregivers, and 27 clinicians. We identified interdependencies between the predischarge preparation, discharge education, and postdischarge follow-up care phases that must be coordinated for effective discharge care transitions. We identified several factors that could lead to fragmented discharges, including limited preoperative preparation, ill-defined discharge education, and postoperative plans. To address these, clinicians often performed behind-the-scenes work, including offering informal preoperative preparation, tailoring discharge education, and personalizing postdischarge follow-up plans. As a result, majority of patients reported high satisfaction with care transitions and their positive impact on their home recovery.

Discussion and conclusions
Articulation work by clinicians (ie, behind the scenes work) is critical for ensuring safety, care continuity, and overall patient experience during care transitions. We discuss key evidence-based considerations for re-engineering postsurgical discharge workflows and re-designing discharge interventions.
Beta-Glucuronidase Activity: Another Source of Ethyl Glucuronide
Authors: Müller Alexander , Aboutara Nadine , Jungen Hilke , Szewczyk Anne , Piesch Melina , Iwersen-Bergmann Stefanie 
Published: June 2022

AbstractNumerous classes of endogenous and xenobiotic compounds are conjugated to uridine-5′-diphospho (UDP)-alpha-D-glucuronic acid which is catalyzed by human UDP-Glucuronosyltransferases (UGTs). The resulting beta-D-glucuronides can be hydrolyzed to β-D-glucuronic acid and the corresponding aglycone in a configuration retaining manner by beta-glucuronidases (GUSBs), which are widely distributed in mammalians, microbiota, insects, molluscs, nematodes, fishes and plants. This study investigates GUSBs’ activity in the presence of ethanol (0–70% by volume) using different β-D-glucuronides (phenolphthalein-β-D-glucuronide, 4-nitrophenol-β-D-glucuronide, morphine-3-O-β-D-glucuronide, quercetin-3-O-β-D-glucuronide and 1-/2-propyl-β-D-glucuronide) as substrates. It was found that β-D-ethyl glucuronide (EtG), which is a minor UGT-derived metabolite of ethanol in man and one of the most frequently used biomarkers of alcohol consumption today, builds up from all investigated β-D-glucuronides by means of GUSBs in the presence of ethanol. The glucuronyl transfer reaction, which was neither detected in the absence of ethanol nor in absence of GUSBs, is minor at ethanol concentrations which are commonly observed in blood and tiβues after consumption of alcoholic beverages, but predominant at higher concentrations of ethanol. In spite of in vitro characteristics, our observations point to an additional biochemical path and another source of EtG, which should be further evaluated in the context of alcohol biomarker applications. The detection of EtG in several settings independent from of human UGT-metabolism (e.g. EtG post post-collection synthesis in E.coli coli-contaminated urine samples, EtG in wine and ethanolic herbal preparations) can be explained by the described mechanism.
Deciphering the function and evolution of the target of rapamycin signaling pathway in microalgae
Authors: Mallén-Ponce Manuel J , Pérez-Pérez María Esther , Crespo José L 
Published: June 2022

AbstractMicroalgae constitute a highly diverse group of photosynthetic microorganisms that are widely distributed on Earth. The rich diversity of microalgae arose from endosymbiotic events that took place early in the evolution of eukaryotes and gave rise to multiple lineages including green algae, the ancestors of land plants. In addition to their fundamental role as the primary source of marine and freshwater food chains, microalgae are essential producers of oxygen on the planet and a major biotechnological target for sustainable biofuel production and CO2 mitigation. Microalgae integrate light and nutrient signals to regulate cell growth. Recent studies identified the target of rapamycin (TOR) kinase as a central regulator of cell growth and a nutrient sensor in microalgae. TOR promotes protein synthesis and regulates processes that are induced under nutrient stress such as autophagy and the accumulation of triacylglycerol and starch. A detailed analysis of representative genomes from the entire microalgal lineage revealed that the highly conserved central components of the TOR pathway are likely to have been present in the last eukaryotic common ancestor, and the loss of specific TOR signaling elements at an early stage in the evolution of microalgae. Here we examine the evolutionary conservation of TOR signaling components in diverse microalgae and discuss recent progress of this signaling pathway in these organisms.
Gravitational torques dominate the dynamics of accreted gas at z &gt; 2
Authors: Cadiou Corentin , Dubois Yohan , Pichon Christophe 
Published: June 2022

ABSTRACT
Galaxies form from the accretion of cosmological infall of gas. In the high redshift Universe, most of this gas infall is expected to be dominated by cold filamentary flows which connect deep down inside haloes, and, hence, to the vicinity of galaxies. Such cold flows are important since they dominate the mass and angular momentum acquisition that can make up rotationally-supported discs at high-redshifts. We study the angular momentum acquisition of gas into galaxies, and in particular, the torques acting on the accretion flows, using hydrodynamical cosmological simulations of high-resolution zoomed-in haloes of a few $10^{11}\, \rm M_\odot$ at z = 2. Torques can be separated into those of gravitational origin, and hydrodynamical ones driven by pressure gradients. We find that coherent gravitational torques dominate over pressure torques in the cold phase, and are hence responsible for the spin-down and realignment of this gas. Pressure torques display small-scale fluctuations of significant amplitude, but with very little coherence on the relevant galaxy or halo-scale that would otherwise allow them to effectively re-orientate the gas flows. Dark matter torques dominate gravitational torques outside the galaxy, while within the galaxy, the baryonic component dominates. The circum-galactic medium emerges as the transition region for angular momentum re-orientation of the cold component towards the central galaxy’s mid-plane.
Accretion history of AGN: Estimating the host galaxy properties in X-ray luminous AGN from z = 0–3
Authors: Coleman Brandon , Kirkpatrick Allison , Cooke Kevin C , Glikman Eilat , La Massa Stephanie , Marchesi Stefano , Peca Alessandro , Treister Ezequiel , Auge Connor , Urry C Megan , Sanders Dave , Turner Tracey Jane , Ananna Tonima Tasnim 
Published: June 2022

ABSTRACT
We aim to determine the intrinsic far-Infrared (far-IR) emission of X-ray-luminous quasars over cosmic time. Using a 16 deg2 region of the Stripe 82 field surveyed by XMM-Newton and Herschel Space Observatory, we identify 2905 X-ray luminous (LX &gt; 1042 erg/s) active galactic nuclei (AGN) in the range z ≈ 0–3. The IR is necessary to constrain host galaxy properties such as star formation rate (SFR) and gas mass. However, only 10 per cent of our AGN are detected both in the X-ray and IR. Because 90 per cent of the sample is undetected in the far-IR by Herschel, we explore the mean IR emission of these undetected sources by stacking their Herschel/SPIRE images in bins of X-ray luminosity and redshift. We create stacked spectral energy distributions from the optical to the far-IR, and estimate the median SFR, dust mass, stellar mass, and infrared luminosity using a fitting routine. We find that the stacked sources on average have similar SFR/Lbol ratios as IR detected sources. The majority of our sources fall on or above the main sequence line suggesting that X-ray selection alone does not predict the location of a galaxy on the main sequence. We also find that the gas depletion time scales of our AGN are similar to those of dusty star forming galaxies. This suggests that X-ray selected AGN host high star formation and that there are no signs of declining star formation.
Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing
Authors: Katanski Christopher D , Watkins Christopher P , Zhang Wen , Reyer Matthew , Miller Samuel , Pan Tao 
Published: June 2022

Abstract
Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
Luminal androgen receptor breast cancer subtype and investigation of the microenvironment and neoadjuvant chemotherapy response
Authors: Thompson Kevin J , Leon-Ferre Roberto A , Sinnwell Jason P , Zahrieh David M , Suman Vera J , Metzger Filho Otto , Asad Sarah , Stover Daniel G , Carey Lisa , Sikov William M , Ingle James N , Liu Minetta C , Carter Jodi M , Klee Eric W , Weinshilboum Richard M , Boughey Judy C , Wang Liewei , Couch Fergus J , Goetz Matthew P , Kalari Krishna R 
Published: June 2022

Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with low overall survival rates and high molecular heterogeneity; therefore, few targeted therapies are available. The luminal androgen receptor (LAR) is the most consistently identified TNBC subtype, but the clinical utility has yet to be established. Here, we constructed a novel genomic classifier, LAR-Sig, that distinguishes the LAR subtype from other TNBC subtypes and provide evidence that it is a clinically distinct disease. A meta-analysis of seven TNBC datasets (n = 1086 samples) from neoadjuvant clinical trials demonstrated that LAR patients have significantly reduced response (pCR) rates than non-LAR TNBC patients (odds ratio = 2.11, 95% CI: 1.33, 2.89). Moreover, deconvolution of the tumor microenvironment confirmed an enrichment of luminal epithelium corresponding with a decrease in basal and myoepithelium in LAR TNBC tumors. Increased immunosuppression in LAR patients may lead to a decreased presence of cycling T-cells and plasma cells. While, an increased presence of myofibroblast-like cancer-associated cells may impede drug delivery and treatment. In summary, the lower levels of tumor infiltrating lymphocytes (TILs), reduced immune activity in the micro-environment, and lower pCR rates after NAC, suggest that new therapeutic strategies for the LAR TNBC subtype need to be developed.