Miracle-dz/UniFAR-FTUs huggingface dataset:
It is still PCP that can stand for Pneumocystis pneumonia: Appeal for generalized use of only one acronym.

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.
Prognosis according to clinical and pathologic lymph node status in breast cancer patients who underwent sentinel lymph node biopsy alone after neoadjuvant therapy

This study aimed to evaluate the prognosis of breast cancer patients who received neoadjuvant chemotherapy and underwent sentinel lymph node biopsy (SLNB) alone as axillary surgery regardless of their clinical and pathological lymph node status. We reviewed the records of 1,795 patients from Asan Medical Center who were diagnosed with stage I–III breast cancer and received neoadjuvant chemotherapy during 2003–2014. We selected 760 patients who underwent SLNB alone as axillary surgery and divided these patients into four groups according to their clinical lymph node (cN) and pathological lymph node (pN) status: cN(-)pN(-) (n = 377), cN(-)pN(+) (n = 33), cN(+)pN(-) (n = 242), and cN(+)pN(+) (n = 108). We then compared axillary lymph node recurrence, locoregional recurrence (LRR), distant metastasis-free survival (DMFS), and overall survival (OS) among the four groups using Kaplan–Meier analysis. We compared prognosis between the cN(-)pN(-) and cN(+)pN(-) groups to determine whether SLNB alone is an adequate treatment modality even in patients with cN positive pathology before neoadjuvant therapy but SLNB-negative pathology after NAC. The 5-year axillary recurrence rates in the cN(-)pN(-) and cN(+)pN(-) groups were 1.4% and 2.9%, respectively, and there was no significant difference between the two groups (p = 0.152). The axillary recurrence and LRR rates were significantly different among the four groups, with the pN-negative groups (cN[–]pN[–], cN[+]pN[–]) showing lower recurrence rates. DMFS and OS were also significantly different among the four groups, with the cN negative groups (cN[–]pN[–], cN[–]pN[+]) showing improved survival rates. Our study findings suggest that SLNB alone was associated with lower LRR rates even in patients with cN positive pathology before neoadjuvant therapy but cN negative pathology after SLNB. Moreover, recurrence and survival rates differ significantly according to clinical and pathological lymph node status.
Memory and Executive Functions Subserving Judgments of Learning: Cognitive Reorganization After Traumatic Brain Injury

ABSTRACT We investigated relationships between psychometric measures of memory, executive functions (EFs), and task-based measures of Judgments of Learning (JOLs) in individuals with and without Traumatic Brain Injury (TBI), to study functional reorganization after TBI. We hypothesized that, in controls, accuracy of immediate JOLs would be associated with short-term memory and EFs (but not long-term memory, LTM), while accuracy of delayed JOLs would be associated primarily with LTM. We hypothesized that those with good recovery from TBI would demonstrate functional reorganization of the relationships between memory, EFs, and JOLs. Eighteen individuals with TBI and 18 matched controls completed eight neuropsychological tests of memory and EFs. They studied word-pairs, made immediate and delayed JOLs, and took a cued-recall test for the studied word-pairs. Stepwise regression and Lasso analyses generated a predictive model of JOL accuracy for each group. Accuracy of immediate JOLs in controls was predicted by short-term memory, inhibition, switching, and cognitive fluency, while accuracy of delayed JOLs was predicted by verbal recall. In individuals with TBI, inhibition predicted immediate JOL accuracy and switching predicted delayed JOL accuracy. Cognitive reorganization in those with good long-term recovery from TBI may account for the ability to make JOLs with accuracy similar to controls.
A systematic review of narrative interventions: Lessons for countering anti-vaccination conspiracy theories and misinformation

Even if a small portion of the population refuses vaccination due to anti-vaccination conspiracy theories or misinformation, this poses a threat to public health. We argue that addressing conspiracy theories with only corrective information is not enough. Instead, considering that they are complex narratives embedded in personal and cultural worldviews, they should be encountered with counternarratives. To identify existing narrative interventions aimed at countering anti-vaccination conspiracy theories and, more generally, map prerequisites for a narrative intervention to be successful, we present a systematic review of experimental effects of exposure to pro-vaccine narratives on a range of vaccination outcomes, based on 17 studies and 97 comparisons. We did not find any narrative interventions aimed directly at conspiracy theories. However, the review allowed us to make evidence-based recommendations for future research and for public communicators. This might help pro-vaccine communication match anti-vaccine communication in its potential to spread and go viral.
Successful live birth after in vitro maturation treatment in a patient with autoimmune premature ovarian failure: a case report and review of the literature

Abstract Objective We report a successful live birth after oocytes in vitro maturation (IVM) and fresh embryo transfer in a patient with autoimmune premature ovarian failure (POF) and performed a review of the literature of livebirths obtained after oocytes IVM treatment in this indication. Methods The patient was a 24-year-old woman with autoimmune POF diagnosed post-partum, who developed autoimmune polyglandular syndrome with serum anti-ovarian and anti-21-hydroxylase antibodies. The patient had typical symptoms of POF: secondary amenorrhea with hypoestrogenism, elevated gonadotropins and infertility; however, the serum anti-Müllerian hormone level and total antral follicle count remained normal. IVM of immature oocytes was performed after the administration of 150 IU highly purified human menopausal gonadotropin for three consecutive days and an injection of 10,000 IU human chorionic gonadotropin to trigger ovulation. Results The six oocyte–cumulus complexes collected matured in vitro. After intracytoplasmic sperm injection (ICSI), five embryos were obtained. Pregnancy was achieved after the fresh transfer of two embryos and appropriate endometrial preparation. A normal female child was delivered following a 37-weeks pregnancy characterized by the onset of adrenal insufficiency and unstable diabetes. Conclusions We report a successful livebirth after IVM treatment in a patient with autoimmune premature ovarian failure (POF). Management of reproductive age women with autoimmune pathology requires fertility counseling. Early diagnosis of autoimmune POF is important for early conception and oocyte preservation, because the only other option at present is ovum donation.
Distribution of molecular strains of Mycobacterium tuberculosis in an intermediate burden Asia Pacific city

Abstract Hong Kong is an intermediate tuberculosis (TB) burden city in Asia Pacific with slow decline of case notification in the last decade. By 24-loci mycobacterial interspersed repetitive units – variable number of tandem repeats genotyping, we examined 534 Mycobacterium tuberculosis isolates collected from culture-positive hospitalised TB patients in a 1.7 million population geographic region in the city. Overall, 286 (75%) were classified as Beijing genotype, of which 216 (76%) and 59 (21%) belonged to modern and ancient sub-lineage, respectively. Only two cases were genetically clustered while spatial clustering was absent. Male gender, permanent residency in Hong Kong and born in Hong Kong or Mainland China were associated with Beijing genotype. The high prevalence of Beijing modern lineage was similar to that in East Asia, which reflected the pattern resulting from population migration. The paucity of clustering suggested that reactivation accounted for most of the TB disease cases, which was and echoed by observation that half were 60 years old or above, and the presence of co-morbid medical conditions. The predominance of reactivation TB cases in intermediate burden localities implies that the detection and control of latent TB infection would be the major challenge in achieving TB elimination.
Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize

Traditional phenotyping methods, coupled with genetic mapping in segregating populations, have identified loci governing complex traits in many crops. Unoccupied aerial systems (UAS)‐based phenotyping has helped to reveal a more novel and dynamic relationship between time‐specific associated loci with complex traits previously unable to be evaluated. Over 1,500 maize (Zea mays L.) hybrid row plots containing 280 different replicated maize hybrids from the Genomes to Fields (G2F) project were evaluated agronomically and using UAS in 2017. Weekly UAS flights captured variation in plant heights during the growing season under three different management conditions each year: optimal planting with irrigation (G2FI), optimal dryland planting without irrigation (G2FD), and a stressed late planting (G2LA). Plant height of different flights were ranked based on importance for yield using a random forest (RF) algorithm. Plant heights captured by early flights in G2FI trials had higher importance (based on Gini scores) for predicting maize grain yield (GY) but also higher accuracies in genomic predictions which fluctuated for G2FD (−0.06∼0.73), G2FI (0.33∼0.76), and G2LA (0.26∼0.78) trials. A genome‐wide association analysis discovered 52 significant single nucleotide polymorphisms (SNPs), seven were found consistently in more than one flights or trial; 45 were flight or trial specific. Total cumulative marker effects for each chromosome's contributions to plant height also changed depending on flight. Using UAS phenotyping, this study showed that many candidate genes putatively play a role in the regulation of plant architecture even in relatively early stages of maize growth and development.
Added mass in rat plantaris muscle causes a reduction in mechanical work.

Most of what we know about whole muscle behaviour comes from experiments on single fibres or small muscles that are scaled up in size without considering the effects of the additional muscle mass. Previous modelling studies have shown that tissue inertia acts to slow the rate of force development and maximum velocity of muscle during shortening contractions and decreases the work and power per cycle during cyclic contractions; however, these results have not yet been confirmed by experiments on living tissue. Therefore, in this study we conducted in situ work-loop experiments on rat plantaris muscle to determine the effects of increasing the mass of muscle on mechanical work during cyclic contractions. We additionally simulated these experimental contractions using a mass-enhanced Hill-type model to validate our previous modelling work. We found that greater added mass resulted in lower mechanical work per cycle relative to the unloaded trials in which no mass was added to the muscle (p=0.041 for both 85% and 123% increases in muscle mass). We additionally found that greater strain resulted in lower work per cycle relative to unloaded trials at the same strain to control for length change and velocity effects on the work output, possibly due to greater accelerations of the muscle mass at higher strains. These results confirm that tissue mass reduces muscle mechanical work at larger muscle sizes, and that this effect is likely amplified for lower activations.
“More than words” – Longitudinal linguistic changes in the works of a writer diagnosed with semantic dementia

ABSTRACT Leveraging recent advances in automated language analysis and anovel statistical approach utilizing an independent control group, we explored changes in lexical output across two published works of a man diagnosed with semantic dementia. We found significant increase in adverb usage and decline in familiarity, meaningfulness, age of acquisition and co-occurrence probability over 2 years. Collectively, these indices suggest that WR’s narrative structure became progressively simpler, lexically less sophisticated, and that words commonly associated together no longer appeared in close proximity. Our study illustrates how degeneration of the semantic knowledge base impacts the production, content, and quality of literary works.
Differences in the mass and quality of the quadriceps with age and sex and their relationships with knee extension strength

Although muscle quality evaluations are currently considered important for diagnosing sarcopenia, data from the general population are lacking. This study used mid‐thigh computed tomography measurements to evaluate age‐related and sex‐related differences in quadriceps femoris muscle quality and mass and their relationships with knee extension strength (KES).
Alveolar Bone Marrow Gli1+ Stem Cells Support Implant Osseointegration

Osseointegration is the key issue for implant success. The in vivo properties of cell populations driving the osseointegration process have remained largely unknown. In the current study, using tissue clearing–based 3-dimensional imaging and transgenic mouse model-based lineage tracing methods, we identified Gli1+ cells within alveolar bone marrow and their progeny as the cell population participating in extraction socket healing and implant osseointegration. These Gli1+ cells are surrounding blood vessels and do not express lineage differentiation markers. After tooth extraction and delayed placement of a dental implant, Gli1+ cells were activated into proliferation, and their descendants contributed significantly to new bone formation. Ablation of Gli1+ cells severely compromised the healing and osseointegration processes. Blockage of canonical Wnt signaling resulted in impaired recruitment of Gli1+ cells and compromised bone healing surrounding implants. Collectively, these findings demonstrate that Gli1+ cells surrounding alveolar bone marrow vasculature are stem cells supporting dental implant osseointegration. Canonical Wnt signal plays critical roles in regulating Gli1+ stem cells.
The epidemiology of acute kidney injury in critically ill patients in the Gansu Province: The EACG study

To investigate the epidemiology of acute kidney injury and to clarify the risk factors associated with the prognosis of acute kidney injury in critically ill patients in the Gansu Province. This was a multicenter, retrospective study. The clinical data of all patients from January 1, 2017, to December 31, 2019, in the intensive care unit of the selected hospitals were screened. Descriptive statistical analysis was performed first, and then the patients were divided into a survival group and a nonsurvival group based on survival status at discharge. Univariate and multivariate logistic regression analyses were used to determine the risk factors for in-hospital mortality in patients with acute kidney injury. (1) Among the 8106 patients admitted, a total of 3019 patients were excluded according to the exclusion criteria. Among the included patients, 890 patients met the diagnostic criteria for AKI, with an incidence of 17.5% and mortality of 41.3%. (2) Logistic regression analysis showed that sex, age, AKI stage, infection, cardio-pulmonary resuscitation, cardiac output, mechanical ventilation, diuretics, white blood cells, platelets, blood urea nitrogen, prothrombin time, and activated partial thromboplastin time were significantly associated with the prognosis of acute kidney injury (p < 0.05). Large-scale epidemiological data from several representative general hospitals in the Gansu Province showed that the incidence and mortality of acute kidney injury in intensive care units were still very high. Trial registration: the Chinese Clinical Trial Registry number is ChiCTR1800016945. Date of registration: 4 July 2018.
ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts

Abstract ReFOLD3 is unique in its application of gradual restraints, calculated from local model quality estimates and contact predictions, which are used to guide the refinement of theoretical 3D protein models towards the native structures. ReFOLD3 achieves improved performance by using an iterative refinement protocol to fix incorrect residue contacts and local errors, including unusual bonds and angles, which are identified in the submitted models by our leading ModFOLD8 model quality assessment method. Following refinement, the likely resulting improvements to the submitted models are recognized by ModFOLD8, which produces both global and local quality estimates. During the CASP14 prediction season (May–Aug 2020), we used the ReFOLD3 protocol to refine hundreds of 3D models, for both the refinement and the main tertiary structure prediction categories. Our group improved the global and local quality scores for numerous starting models in the refinement category, where we ranked in the top 10 according to the official assessment. The ReFOLD3 protocol was also used for the refinement of the SARS-CoV-2 targets as a part of the CASP Commons COVID-19 initiative, and we provided a significant number of the top 10 models. The ReFOLD3 web server is freely available at https://www.reading. ac.uk/bioinf/ReFOLD/.
An investigation of the effects of different shift schedules on the fatigue and sleepiness of officers on oil tankers during cargo handling operations

Abstract Cargo handling is an operation, which requires a high level of performance from the officer of the watch (OOW). This study aimed to investigate the effect of different shift schedules on sleep quality, cognitive performance, and sleepiness of 139 OOWs on oil tankers with 4on–8off shifts, during the first shift of cargo handling. Sleep quality (Pittsburgh Sleep Quality Index (PSQI)), level of sleepiness (the Karolinska Sleepiness Scale (KSS)), Psychomotor Vigilance Task (PVT), and Arrow Flanker task performance were examined. The results showed that OOWs with (00:00–04:00, 12:00–16:00) and (04:00–08:00, 16:00–20:00) shifts had impaired cognitive performance and higher sleepiness during the cargo handling operation, and they also experienced impaired sleep quality. The results demonstrated that the circadian rhythm and homeostatic sleep drive have a greater impact on cognitive performance and sleepiness than time on shifts. These results suggest that allocating rest hours immediately before the cargo handling operation may reduce the risk of fatigue. Practitioner Summary: To the best of our knowledge, this maritime field study shows for the first time the prevalence of seafarers’ sleepiness and cognitive performance while on duty during cargo handling, using a pre-post shift comparison between three different shifts. The results show the negative effects of keeping watch at night on sleep quality, sleepiness, and the impaired cognitive performance both in the day and the night shifts.
Single-cell multiomics dissection of basal and antigen-specific activation states of CD19-targeted CAR T cells

Background Autologous T cells engineered to express a chimeric antigen receptor (CAR) specific for CD19 molecule have transformed the therapeutic landscape in patients with highly refractory leukemia and lymphoma, and the use of donor-generated allogeneic CAR T is paving the way for further breakthroughs in the treatment of cancer. However, it remains unknown how the intrinsic heterogeneities of these engineered cells mediate therapeutic efficacy and whether allogeneic products match the effectiveness of autologous therapies. Methods Using single-cell mRNA sequencing in conjunction with CITE-seq, we performed multiomics characterization of CAR T cells generated from healthy donor and patients with acute lymphoblastic leukemia. CAR T cells used in this study were manufactured at the University of Pennsylvania through lentiviral transduction with a CD19-4-1BB-CD3ζ construct. Besides the baseline condition, we engineered NIH-3T3 cells with human CD19 or mesothelin expression to conduct ex vivo antigen-specific or non-antigen stimulation of CAR T cells through 6-hour coculture at a 1:1 ratio. Results We delineated the global cellular and molecular CAR T landscape and identified that transcriptional CAR tonic signaling was regulated by a mixture of early activation, exhaustion signatures, and cytotoxic activities. On CD19 stimulation, we illuminated the disparities of CAR T cells derived from different origins and found that donor CAR T had more pronounced activation level in correlation with the upregulation of major histocompatibility complex class II genes compared with patient CAR T cells. This finding was independently validated in additional datasets from literature. Furthermore, GM-CSF(CSF2) expression was found to be associated with functional gene productions, but it induced little impact on the CAR T activation. Conclusions Through integrated multiomics profiling and unbiased canonical pathway analyses, our results unveil heterogeneities in the transcriptional, phenotypic, functional, and metabolic profiles of donor and patient CAR T cells, providing mechanistic basis for ameliorating clinical outcomes and developing next-generation ‘off- the-shelf’ allogeneic products.
Strongly Anharmonic Octahedral Tilting in Two-Dimensional Hybrid Halide Perovskites

Recent investigations of two-dimensional (2D) hybrid organic–inorganic halide perovskites (HHPs) indicate that their optical and electronic properties are dominated by strong coupling to thermal fluctuations. While the optical properties of 2D-HHPs have been extensively studied, a comprehensive understanding of electron–phonon interactions is limited because little is known about their structural dynamics. This is partially because the unit cells of 2D-HHPs contain many atoms. Therefore, the thermal fluctuations are complex and difficult to elucidate in detail. To overcome this challenge, we use polarization-orientation Raman spectroscopy and ab initio calculations to compare the structural dynamics of the prototypical 2D-HHPs [(BA)2PbI4 and (PhE)2PbI4] to their three-dimensional (3D) counterpart, MAPbI3. Comparison to the simpler, 3D MAPbI3 crystal shows clear similarities with the structural dynamics of (BA)2PbI4 and (PhE)2PbI4 across a wide temperature range. The analogy between the 3D and 2D crystals allows us to isolate the effect of the organic cation on the structural dynamics of the inorganic scaffold of the 2D-HHPs. Furthermore, using this approach, we uncover the mechanism of the order–disorder phase transition of (BA)2PbI4 (274 K) and show that it involves relaxation of octahedral tilting coupled to anharmonic thermal fluctuations. These anharmonic fluctuations are important because they induce charge carrier localization and affect the optoelectronic performance of these materials.