julilili42/papers huggingface dataset:
Complex variations of X-ray polarization in the X-ray pulsar LS V +44 17/RX J0440.9+4431
2023-06-28

We report on ixpe observations of the Be-transient X-ray pulsar LS V +44 17/RX J0440.9+4431 at two luminosity levels during the giant outburst in January--February 2023. Considering the observed spectral variability and changes in the pulse profiles, the source was likely caught in super- and sub-critical states with significantly different emission region geometry, associated with the presence of accretion columns and hot spots, respectively. We focus here on the pulse-phase resolved polarimetric analysis and find that the observed dependencies of the polarization degree and polarization angle (PA) on pulse phase are indeed drastically different for the two observations. The observed differences, if interpreted within the framework of the rotating vector model (RVM), imply dramatic variations of the spin axis inclination and the position angle and the magnetic colatitude by tens of degrees within just a few days separating the observations. We suggest that the apparent changes in the observed PA phase dependence are predominantly related to the presence of a polarized unpulsed component in addition to the polarized radiation associated with the pulsar itself. We show that the observed PA phase dependence in both observations can then be explained with a single set of RVM parameters defining the pulsar's geometry. We also suggest that the additional polarized component is likely produced by scattering of the pulsar radiation off the equatorial disk wind.
Visual and Physiological Optics: introduction to the joint feature issue in Biomedical Optics Express and Journal of the Optical Society of America A
2023-06-28

This feature issue collects articles presented at the tenth Visual and Physiological Optics meeting (VPO2022), held August 29–31, 2022, in Cambridge, UK. This joint feature issue between Biomedical Optics Express and Journal of the Optical Society of America A includes articles that cover the broad range of topics addressed at the meeting and examples of the current state of research in the field.
Oral health-related quality of life and depressive symptoms in older adults: Longitudinal associations of the English Longitudinal Study of Ageing (ELSA)
2023-06-28

Abstract Background Little is known about the relationship between oral health status and depressive symptoms in older adults in England. The aim of this study was to examine the longitudinal association between oral health parameters and depressive symptoms in older adults in England. Methods Data were obtained from the English Longitudinal Study of Aging (ELSA), which included information on self-rated oral health, oral impairment in daily life (Oral Impacts on Daily Performances, OIDP), and depressive symptoms (Center for Epidemiologic Studies Depression Scale, CES-D) in 6790 adults aged ≥ 50 years. Wave 3 data were used as baseline, while Waves 5 and 7 were used for follow-up assessments. Logistic regression was used to determine whether depressive symptoms at baseline predicted self-rated oral health and OIDP and whether oral health status (at baseline) was associated with the development of depressive symptoms at follow-up assessment. Results Participants with poor self-rated oral health were at higher risk of developing depressive symptoms, even after adjusting for behavioural, clinical, and sociodemographic characteristics (OR = 1.69, 95% CI 1.38–2.07). Similar results were reported for the presence of one or more oral conditions: The OR for developing depressive symptoms at Wave 5 or 7 was 2.19 (95% CI 1.62–2.96). Participants with depressive symptoms at baseline were more likely to report poor self-rated oral health (OR = 1.93, 95% CI 1.52–2.44) or one or more oral impacts (OR = 1.86, 95% CI 1.45–2.40) at follow-up than those without depressive symptoms. Conclusions In the present study, a bidirectional association was found between depressive symptoms and poor oral health in older adults. Maintaining good oral health in older adults may be a protective factor against depressive symptoms. Therefore, more attention should be paid to promoting oral health awareness in older adults, including encouraging regular dental checkups, proper toothbrushing and flossing techniques, and healthy lifestyles.
True Crime Television as ‘Popular Legality’: Affect, Testimonial Injustice, and the Criminal (In)Justice System in Ava DuVernay’s When They See Us
2023-06-28

This article examines the Netflix true crime series When They See Us (2019) as a form of “popular legality” (Olson 2022). I argue that the show criticizes structural racism in the US criminal justice system and emphasizes this critique on a level of affect. More precisely, it is through an affective engagement of the audience with the show’s protagonists that When They See Us highlights how Black and Latinx communities are discriminated by US law and the criminal justice system. It thereby not only depicts African American and Latinx legal identities as marginalized by the law and legal system, but makes viewers able to feel them to be so. In addition, I argue that the show negotiates issues of testimonial injustice as one form of discrimination against People of Color in the US legal system. This negotiation of testimonial injustice also primarily takes place on a level of affect by inviting the audience to feel the effects that testimonial injustice has on the show’s protagonists.
X-ray polarimetry of X-ray pulsar X Persei: another orthogonal rotator?
2023-06-29

ABSTRACT X Persei is a persistent low-luminosity X-ray pulsar of period of ≈ 835 s in a Be binary system. The field strength at the neutron star surface is not known precisely, but indirect signs indicate a magnetic field above 1013 G, which makes the object one of the most magnetized known X-ray pulsars. Here we present the results of observations X Persei performed with the Imaging X-ray Polarimetry Explorer (IXPE). The X-ray polarization signal was found to be strongly dependent on the spin phase of the pulsar. The energy-averaged polarization degree in 3–8 keV band varied from several to ∼20 per cent over the pulse with a phase dependence resembling the pulse profile. The polarization angle shows significant variation and makes two complete revolutions during the pulse period, resulting in nearly nil pulse-phase averaged polarization. Applying the rotating vector model to the IXPE data we obtain the estimates for the rotation axis inclination and its position angle on the sky, as well as for the magnetic obliquity. The derived inclination is close to the orbital inclination, reported earlier for X Persei. The polarimetric data imply a large angle between the rotation and magnetic dipole axes, which is similar to the result reported recently for the X-ray pulsar GRO J1008−57. After eliminating the effect of polarization angle rotation over the pulsar phase using the best-fitting rotating vector model, the strong dependence of the polarization degree with energy was discovered, with its value increasing from 0 at ∼2 keV to 30per cent at 8 keV.
The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections
2023-06-29

Controlled human malaria infections (CHMI) are a valuable tool to study parasite gene expression in vivo under defined conditions. In previous studies, virulence gene expression was analyzed in samples from volunteers infected with the Plasmodium falciparum (Pf) NF54 isolate, which is of African origin. Here, we provide an in-depth investigation of parasite virulence gene expression in malaria-naïve European volunteers undergoing CHMI with the genetically distinct Pf 7G8 clone, originating in Brazil. Differential expression of var genes, encoding major virulence factors of Pf, PfEMP1s, was assessed in ex vivo parasite samples as well as in parasites from the in vitro cell bank culture that was used to generate the sporozoites (SPZ) for CHMI (Sanaria PfSPZ Challenge (7G8)). We report broad activation of mainly B-type subtelomeric located var genes at the onset of a 7G8 blood stage infection in naïve volunteers, mirroring the NF54 expression study and suggesting that the expression of virulence-associated genes is generally reset during transmission from the mosquito to the human host. However, in 7G8 parasites, we additionally detected a continuously expressed single C-type variant, Pf7G8_040025600, that was most highly expressed in both pre-mosquito cell bank and volunteer samples, suggesting that 7G8, unlike NF54, maintains expression of some previously expressed var variants during transmission. This suggests that in a new host, the parasite may preferentially express the variants that previously allowed successful infection and transmission. Trial registration: ClinicalTrials.gov - NCT02704533 ; 2018-004523-36
Discounting future reward in an uncertain world.
2023-06-29

Humans discount delayed relative to more immediate reward. A plausible explanation is that impatience arises partly from uncertainty, or risk, implicit in delayed reward. Existing theories of discounting-as-risk focus on a probability that delayed reward will not materialize. By contrast, we examine how uncertainty in the magnitude of delayed reward contributes to delay discounting. We propose a model wherein reward is discounted proportional to the rate of random change in its magnitude across time, termed <i>volatility</i>. We find evidence to support this model across three experiments (total <i>N</i> = 158). First, using a task where participants chose when to sell products, whose price dynamics they previously learned, we show discounting increases in line with price volatility. Second, we show that this effect pertains over naturalistic delays of up to 4 months. Using functional magnetic resonance imaging, we observe a volatility-dependent decrease in functional hippocampal-prefrontal coupling during intertemporal choice. Third, we replicate these effects in a larger online sample, finding that volatility discounting within each task correlates with baseline discounting outside of the task. We conclude that delay discounting partly reflects time-dependent uncertainty about reward magnitude, that is volatility. Our model captures how discounting adapts to volatility, thereby partly accounting for individual differences in impatience. Our imaging findings suggest a putative mechanism whereby uncertainty reduces prospective simulation of future outcomes.
Time and visual-spatial illusions: Evidence for cross-dimensional interference between duration and illusory size
2023-06-29

Abstract Time and space are intimately related to each other. Previous evidence has shown that stimulus size can affect perceived duration even when size differences are illusory. In the present study, we investigated the effect of visual-spatial illusions on duration judgments in a temporal reproduction paradigm. Specifically, we induced the Ebbinghaus illusion (Exp. 1) and the horizontal-vertical illusion (Exp. 2) during the encoding phase of the target interval or the reproduction phase. The results showed (a) that illusory size affects temporal processing similarly to the way physical size does, (b) that the effect is independent of whether the illusion appeared during encoding or reproduction, and (c) that the interference between size and temporal processing is bidirectional. These results suggest a rather late locus of size-time interference in the processing stream.
Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation
2023-06-29

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α , rhd2α , and pahE . However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10 −2 , 1.80 × 10 −3 , and 3.20 × 10 −3 for rhd3α , rhd2α , and pahE , respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10 −1 ). The other marker genes— rhd3α and pahE— were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.
Mus musculus papillomavirus 1 E8^E2 represses expression of late protein E4 in basal-like keratinocytes via NCoR/SMRT-HDAC3 co-repressor complexes to enable wart formation in vivo
2023-06-29

ABSTRACT High-risk human papillomaviruses (PV) account for approximately 600,000 new cancers per year. The early protein E8^E2 is a conserved repressor of PV replication, whereas E4 is a late protein that arrests cells in G2 and collapses keratin filaments to facilitate virion release. While inactivation of the Mus musculus PV1 (MmuPV1) E8 start codon (E8-) increases viral gene expression, surprisingly, it prevents wart formation in FoxN1 nu/nu mice. To understand this surprising phenotype, the impact of additional E8^E2 mutations was characterized in tissue culture and mice. MmuPV1 and HPV E8^E2 similarly interact with cellular NCoR/SMRT-HDAC3 co-repressor complexes. Disruption of the splice donor sequence used to generate the E8^E2 transcript or E8^E2 mutants (mt) with impaired binding to NCoR/SMRT-HDAC3 activates MmuPV1 transcription in murine keratinocytes. These MmuPV1 E8^E2 mt genomes also fail to induce warts in mice. The phenotype of E8^E2 mt genomes in undifferentiated cells resembles productive PV replication in differentiated keratinocytes. Consistent with this, E8^E2 mt genomes induced aberrant E4 expression in undifferentiated keratinocytes. In line with observations for HPV, MmuPV1 E4-positive cells displayed a shift to the G2 phase of the cell cycle. In summary, we propose that in order to enable both expansion of infected cells and wart formation in vivo , MmuPV1 E8^E2 inhibits E4 protein expression in the basal keratinocytes that would otherwise undergo E4-mediated cell cycle arrest. IMPORTANCE Human papillomaviruses (PVs) initiate productive replication, which is characterized by genome amplification and expression of E4 protein strictly within suprabasal, differentiated keratinocytes. Mus musculus PV1 mutants that disrupt splicing of the E8^E2 transcript or abolish the interaction of E8^E2 with cellular NCoR/SMRT-HDAC3 co-repressor complexes display increased gene expression in tissue culture but are unable to form warts in vivo . This confirms that the repressor activity of E8^E2 is required for tumor formation and genetically defines a conserved E8 interaction domain. E8^E2 prevents expression of E4 protein in basal-like, undifferentiated keratinocytes and thereby their arrest in G2 phase. Since binding of E8^E2 to NCoR/SMRT-HDAC3 co-repressor is required to enable expansion of infected cells in the basal layer and wart formation in vivo , this interaction represents a novel, conserved, and potentially druggable target.
On the role of verb-particle constructions in Old Spanish
2023-06-29

Abstract The present contribution investigates verb-particle constructions formed with atras ‘back(wards)’ in Old Spanish, against the background of the typological change from (mostly) satellite-framed patterns in Latin to the predominantly verb-framed strategies in the Romance languages. The study innovatively combines diachronic Construction Grammar with a functional-onomasiological perspective. This means that VPCs are studied relative to “competing” strategies of motion encoding such as instantiations of the prefix-construction [ re -V] ‘V back’ and newly formed path verbs such as tornar/volver ‘turn/go back’. The diachronic study shows that VPCs are in principle available at all language stages of Spanish. Moreover, the onomasiological perspective suggests that the observed “rise” of VPCs in Old Spanish could in fact be related to constructional micro-changes occurring among path verbs and instantiations of [ re -V]. Within this network of functionally related constructions, VPCs prove to form a transparent and potentially expressive, mostly intransitive pattern to encode directed motion meanings.
Adipokines as Predictive Biomarkers for Training Adaptation in Subjects with Multimorbidity—A Hypothesis-Generating Study
2023-06-29

Background. Physical exercise exerts a positive effect on many chronic conditions, specifically lifestyle-related diseases such as overweight and obesity, type 2 diabetes mellitus (T2DM), cardiovascular conditions and osteoarthritis (OA). As a result of common risk factors, most of these patients present with multiple conditions. Exercise- and disease-related biomarkers, such as adipokines, are emerging tools in training supervision and regulation; however, their significance in subjects with multimorbidities is unknown. Subjects and Methods. To address this issue, adipokines leptin, adiponectin and resistin were assessed in a cohort of subjects with multimorbidities (n = 39) presenting with at least two of the abovementioned conditions or relevant risk factors before and after a six-month exercise and lifestyle intervention program (‘MultiPill-Exercise’), and correlated with training adaptation, namely changes in relative maximum oxygen uptake (V·O2max). Results. There was a significant negative correlation between baseline leptin concentrations and training effect for relative V·O2max (after three months: rho = −0.54, p = 0.020 *; after six months: rho = −0.45, p = 0.013 *), with baseline leptin explaining 35% of the variance in delta relative V·O2max after three months and 23% after six months. Conclusions. Leptin might be a suitable surrogate biomarker in the context of exercise-based lifestyle intervention programs in subjects with multimorbidity.
Construction Grammar meets Hispanic linguistics
2023-06-29

Abstract This chapter offers an introduction to the topic and to the individual contributions of the present volume. First, it presents an evaluation of the general potential of combining (usage-based and cognitively oriented) Construction Grammar with Hispanic (and Romance) linguistics. Further, it aims at highlighting the innovative perspective of Construction Grammar(s) in comparison to more traditional approaches for the linguistic phenomena covered in this volume. The chapter concludes with a brief overview of the structure of the book as well as of the individual contributions.
Two birds with one stone: human SIRPα nanobodies for functional modulation and in vivo imaging of myeloid cells
2023-06-29

Abstract Signal-regulatory protein α (SIRPα) expressed by myeloid cells is of particular interest for therapeutic strategies targeting the interaction between SIRPα and the "don’t eat me" ligand CD47 and as a marker to monitor macrophage infiltration into tumor lesions. To address both approaches, we developed a set of novel human SIRPα (hSIRPα)-specific nanobodies (Nbs). We identified three high-affinity Nbs targeting the hSIRPα/hCD47 interface, thereby enhancing antibody-dependent cellular phagocytosis (ADCP). For non-invasive in vivo imaging, we chose S36 Nb as a non-modulating binder. By quantitative positron emission tomography (PET) in novel hSIRPα/hCD47 knock-in (KI) mice, we demonstrated the applicability of 64 Cu-hSIRPα-S36 Nb to visualize tumor infiltration of myeloid cells. We envision that the hSIRPα-Nbs presented in this study have potential as versatile probes, including novel myeloid-specific checkpoint inhibitors for combinatorial treatment approaches and for in vivo stratification and monitoring of individual responses during cancer immunotherapies.
Clinical Significance of the Stromatic Component in Ovarian Cancer: Quantity Over Quality in Outcome Prediction
2023-06-29

Abstract Background The tumor stroma is composed of a complex network of non-cancerous cells and extracellular matrix elements that collectively are crucial for cancer progression and treatment response. Within the realm of ovarian cancer, the expression of the stromal gene cluster has been linked to poorer progression-free and overall survival rates. However, in the age of precision medicine and genome sequencing, the notion that the simple measurement of tumor-stroma proportion alone can serve as a biomarker for clinical outcome is a topic that continues to generate controversy and provoke discussion. Our current study reveals that it is the quantity of stroma, rather than its quality, that serves as a clinically significant indicator of patient outcome in ovarian cancer. Methods This study leveraged the High-Grade-Serous-Carcinoma (HGSC) cohort of the publicly accessible Cancer Genome Atlas Program (TCGA) along with an independent cohort comprising HGSC clinical specimens in diagnostic and Tissue Microarray formats. Our objective was to investigate the correlation between the Tumor-Stroma-Proportion (TSP) and progression-free survival (PFS), overall survival (OS), and response to chemotherapy. We assessed these associations using H&amp;E-stained slides and tissue microarrays. Our analysis employed semi-parametric models that accounted for age, metastases, and residual disease as controlling factors. Results We found that high TSP (&gt;50% stroma) was associated with significantly shorter progression-free survival (PFS) (p=0.016) and overall survival (OS) (p=0.006). Tumors from patients with chemoresistant tumors were twice as likely to have high TSP as compared to tumors from chemosensitive patients (p=0.012). In tissue microarrays, high TSP was again associated with significantly shorter PFS (p=0.044) and OS (p=0.0001), further confirming our findings. The Area Under the ROC curve for the model predicting platinum was estimated at 0.7644. Conclusions In HGSC, TSP was a consistent and reproducible marker of clinical outcome measures, including PFS, OS, and platinum chemoresistance. Assessment of TSP as a predictive biomarker that can be easily implemented and integrated into prospective clinical trial design and adapted to identify, at time of initial diagnosis, patients who are least likely to benefit long-term from conventional platinum-based cytotoxic chemotherapy treatment.