Miracle-dz/UniFAR-FTUs huggingface dataset:
Mediastinal Metastasis of Breast Cancer Mimicking a Primary Mediastinal Tumor

Case series Patients: Female, 48-year-old • Female, 47-year-old Final Diagnosis: Metastatic breast cancer Symptoms: Edema of left upper limb • no symptom Medication: — Clinical Procedure: Median sternotomy • small incisional biopsy Specialty: Surgery Objective: Challenging differential diagnosis Background: Breast cancer is becoming a common disease in women. It progresses slowly and may recur after a long time. Therefore, when a tumor is found in the chest of a patient with a history of breast cancer, an immediate concern is whether it is a primary tumor or a metastatic tumor. However, mediastinal metastasis is extremely unlikely to occur before lung metastasis, and breast cancer is not likely to have a solitary mediastinal metastasis. Additionally, patients should not undergo invasive procedures unnecessarily, so careful consideration is required. Case Reports: We present 2 cases. In case 1, a 48-year-old woman with a history of breast cancer had a mediastinal tumor. Based on imaging findings, cystic thymoma was suspected. Thoracoscopic intraoperative rapid biopsy showed a lymphocyte-predominant tumor tissue; therefore, the tumor was resected via a median sternotomy. The final pathological diagnosis was breast cancer metastasis. In case 2, a 47-year-old woman who underwent breast cancer resection 15 years earlier was referred for upper limb edema. Based on imaging findings, a left medial vein occlusion due to mediastinal tumor was diagnosed. Our experience in case 1 suggested that a biopsy alone should be performed first. A tumor biopsy was performed through a small transverse neck incision in case 2, and the final diagnosis was metastatic breast cancer of the mediastinum. Conclusions: In patients with a suspected primary mediastinal tumor on imaging, the possibility of a metastatic tumor should be considered if they have a history of breast cancer, regardless of how long in the past it was.
Protease protection assays show polypeptide movement into the SecY channel by power strokes of the SecA ATPase

Bacterial secretory proteins are translocated post‐translationally by the SecA ATPase through the protein‐conducting SecY channel in the plasma membrane. During the ATP hydrolysis cycle, SecA undergoes large conformational changes of its two‐helix finger and clamp domains, but how these changes result in polypeptide movement is unclear. Here, we use a reconstituted purified system and protease protection assays to show that ATP binding to SecA results in a segment of the translocation substrate being pushed into the channel. This motion is prevented by mutation of conserved residues at the finger's tip. Mutation of SecA's clamp causes backsliding of the substrate in the ATP‐bound state. Together, these data support a power stroke model of translocation in which, upon ATP binding, the two‐helix finger pushes the substrate into the channel, where it is held by the clamp until nucleotide hydrolysis has occurred.
Daily Physical Activity and Sedentary Time Assessed by Acceleration Based on Mean Amplitude Deviation among Older People

Accelerometer-derived estimates of physical activity (PA) and sedentary time have been an important methodological focus. However, little is known about the daily activities among older people during their normal lives. Furthermore, some older individuals would like to be more active, yet experience an unmet PA need, which is defined as the desire to engage in more PA but without the opportunity to act on the desire. This study examined the intensity of daily PA and sedentary behavior measured with accelerometers among older people, and whether PA differs between weekdays and weekends and those with and without the experience of unmet PA need, measured with self-reports. A total of 174 community-dwelling older people (64% female) aged 75 to 90 years used an accelerometer for 7 consecutive days during waking hours, and the results were classified for sedentary behavior (thresholds of 0.0167 g), light activity (0.091 g), and moderate-to-vigorous activity (MVPA, 0.414 g) based on mean amplitude deviation (g). We found that during weekdays, older people engaged slightly more in light activity and had less sedentary time than during weekends. In total, 7.6% of the participants perceived an unmet PA need. Accordingly, those with unmet PA needs spent less time in MVPA, especially during weekdays, and they might benefit from PA-enabling interventions.
Quality of Life Changes in Acute Coronary Syndromes Patients: A Systematic Review and Meta-Analysis

There is little up-to-date evidence about changes in quality of life following treatment for acute coronary syndrome (ACS) patients. The main aim of this review was to assess the changes in QoL in ACS patients after treatment. We undertook a systematic review and meta-analysis of quantitative studies. The search included studies that described the change of QoL of ACS patients after receiving treatment options such as percutaneous coronary intervention (PCI), coronary artery bypass grafting (CABG) and medical therapy (MT). We synthesized findings using content analysis and pooled the estimates using meta-analysis. We used the PRISMA guidelines to select and appraise the studies and report the findings. Twenty-nine (29) articles were included in the review. We found a significant improvement of QoL in ACS patients after receiving treatment. Particularly, the meta-analytic association found that the mean QoL of patients diagnosed with ACS was higher after receiving treatment compared to baseline (overall pooled mean difference = 31.88; 95% CI = 31.64–52.11, I2 = 98) with patients on PCI having slightly lower QoL gains (pooled mean difference = 30.22; 95% CI = 29.9–30.53, I2 = 0%) compared to those on CABG (pooled mean difference = 34.01; 95% CI = 33.66–34.37, I2 = 0%). The review confirmed that QoL of ACS patients improved after receiving treatment therapies although varied by the treatment options and patients’ preferences. This suggests the need to perform further study on the QoL, patient preferences and physicians’ decision to prescription of treatment options.
Robust and persistent SARS-CoV-2 infection in the human intestinal brush border expressing cells

ABSTRACT Studies on patients with the coronavirus disease-2019 (COVID-19) have implicated that the gastrointestinal (GI) tract is a major site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We established a human GI tract cell line model highly permissive to SARS-CoV-2. These cells, C2BBe1 intestinal cells with a brush border having high levels of transmembrane serine protease 2 (TMPRSS2), showed robust viral propagation, and could be persistently infected with SARS-CoV-2, supporting the clinical observations of persistent GI infection in COVID-19 patients. Ectopic expression of viral receptors revealed that the levels of angiotensin-converting enzyme 2 (ACE2) expression confer permissiveness to SARS-CoV-2 infection, and TMPRSS2 greatly facilitates ACE2-mediated SARS-CoV-2 dissemination. Interestingly, ACE2 but not TMPRSS2 expression was significantly promoted by enterocytic differentiation, suggesting that the state of enterocytic differentiation may serve as a determining factor for viral propagation. Thus, our study sheds light on the pathogenesis of SARS-CoV-2 in the GI tract.
Effects of Cooling Rate during Quenching and Tempering Conditions on Microstructures and Mechanical Properties of Carbon Steel Flange

This study investigated the mechanical properties of steel in flanges, with the goal of obtaining high strength and high toughness. Quenching was applied alone or in combination with tempering at one of nine combinations of three temperatures TTEM and durations tTEM. Cooling rates at various flange locations during quenching were first estimated using finite element method simulation, and the three locations were selected for mechanical testing in terms of cooling rate. Microstructures of specimens were observed at each condition. Tensile test and hardness test were performed at room temperature, and a Charpy impact test was performed at −46 °C. All specimens had a multiphase microstructure composed of matrix and secondary phases, which decomposed under the various tempering conditions. Decrease in cooling rate (CR) during quenching caused reduction in hardness and strength but did not affect low-temperature toughness significantly. After tempering, hardness and strength were reduced and low-temperature toughness was increased. Microstructures and mechanical properties under the various tempering conditions and CRs during quenching were discussed. This work was based on the properties directly obtained from flanges under industrial processes and is thus expected to be useful for practical applications.
Investigation of prokaryotic immune defense system with quantitative and structural mass spectrometry

Bacteria and archaea have evolved an adaptive and heritable immune defense system comprising a CRISPR (clustered regularly interspaced short palindromic repeats) locus and Cas (CRISPR-associated) proteins that targets mobile genetic elements such as phages and plasmids. The molecular memory of previous infections is transcribed into crRNAs (CRISPR RNAs) which serve as a template to guide the hydrolysis of incoming foreign genetic material. The CRISPR-Cas system is divided into three Types (I, II and III) on the basis of signature cas genes and further subtypes defined by the protein machinery and target specificity. During my PhD work, I investigated the Type I and Type III CRISPR-Cas systems using quantitative and structural mass spectrometry approaches. The first part of this work focused on using relative quantitative approach to study the effect of a cas gene deletion on the expression levels of other Cas proteins in Haloferax volcanii. A comparison between the proteomes of H. volcanii wild type and deletion strains using stable-isotope dimethyl labeling showed that the removal of a cas gene is compensated by an overall increase in the expression of cas gene cluster. In addition, the absolute amounts of Cas protein components in multi-subunit Cascade complexes from H. volcanii and Clostridium thermocellum were determined using intensity based absolute quantification. The results were used to determine the stoichiometry of Cas proteins in these multi-subunit protein complexes which is valuable for the further investigation of molecular interactions within these complexes. Further in this work, the UV induced protein-RNA cross-liking approach was utilized to investigate RNA binding regions in single (recombinant) Cas proteins such as the archaeal and bacterial Cas6b proteins and the Cas7 family proteins from four different organisms. These structural studies were also extended to multi-subunit crRNP complexes such as the Type I-E Cascade complex from E. coli and Type III-A Csm complex from Thermus thermophilus. The information derived from the cross-linking studies could validate several protein-RNA interactions reported earlier in X-ray crystallography studies. In addition to identifying new RNA binding regions in the Cas proteins, the identified cross-links could also be mapped to conserved regions of these proteins within modified RNA binding domains. The results provided unbiased evidence of direct protein-RNA interaction in in vitro and in vivo purified crRNP complexes. Lastly, a lysine directed chemical cross-linking approach is presented for the investigation of protein-protein interactions between different Cas proteins in the C. thermocellum Cascade complex where more than 126 inter-protein interactions were identified. These results constitute the first step towards MS based structural modeling of crRNP complexes.
Do experiments exploring plant diversity – ecosystem functioning relationships inform how biodiversity loss impacts natural ecosystems?

An enormous recent research effort focused on how plant biodiversity (notably species richness) influences ecosystem functioning, usually through experiments in which diversity is varied through random draws of species from a species pool. Such experiments are increasingly used to predict how species losses influence ecosystem functioning in ‘real’ ecosystems. However, this assumes that comparisons of experimental communities with low vs high species richness are analogous to comparisons of natural communities from which species either have or have not been lost. I explore the validity of this assumption, and highlight difficulties in using such experiments to draw conclusions about the ecosystem consequences of biodiversity loss in natural systems. Notably, these experiments do not mimic what happens in real ecosystems either when local extinctions occur or when species losses are offset by gains of new species. Despite limitations, this single experimental approach for studying how biodiversity loss affects ecosystems has often been advocated and implemented at the expense of other approaches; this limits understanding of how natural ecosystems respond to biodiversity loss. I conclude that a broader spectrum of approaches, and more explicit consideration of how species losses and gains operate in concert to influence ecosystems, will help progress this field.
Childhood Maltreatment and Adolescent Cyberbullying Perpetration: A Moderated Mediation Model of Callous—Unemotional Traits and Perceived Social Support

Although childhood maltreatment has been shown to play an important role in adolescent cyberbullying perpetration, little is known about mediating and moderating mechanisms underlying this relationship. The current study investigated the mediating role of callous-unemotional (CU) traits in the association between childhood maltreatment and adolescent cyberbullying perpetration, as well as the moderating role of perceived social support. A total of 2,407 Chinese adolescents (aged 11–16 years, Mage = 12.75 years, SD = 0.58) completed the measures of childhood maltreatment, CU traits, cyberbullying perpetration, and perceived social support. The results showed that CU traits partially mediated the relationship between childhood maltreatment and adolescent cyberbullying perpetration. Furthermore, perceived social support moderated the relationship between childhood maltreatment and CU traits, as well as CU traits and cyberbullying perpetration. Specifically, childhood maltreatment had a greater impact on CU traits for adolescents with higher levels of perceived social support and the predictive function of CU traits on cyberbullying perpetration was stronger for adolescents with low levels of perceived social support.
Carbonic anhydrases enhance activity of endogenous Na‐H exchangers and not the electrogenic Na/HCO3 cotransporter NBCe1‐A, expressed in Xenopus oocytes

According to the HCO3− metabolon hypothesis, direct association of cytosolic carbonic anhydrases (CAs) with the electrogenic Na/HCO3 cotransporter NBCe1‐A speeds transport by regenerating/consuming HCO3− . The present work addresses published discrepancies as to whether cytosolic CAs stimulate NBCe1‐A, heterologously expressed in Xenopus oocytes. We confirm the essential elements of the previous experimental observations, taken as support for the HCO3− metabolon hypothesis. However, using our own experimental protocols or those of others, we find that NBCe1‐A function is unaffected by cytosolic CAs. Previous conclusions that cytosolic CAs do stimulate NBCe1‐A can be explained by an unanticipated stimulatory effect of the CAs on an endogenous Na‐H exchanger. Theoretical analyses show that, although CAs could stimulate non‐ HCO3− transporters (e.g. Na‐H exchangers) by accelerating CO2/ HCO3− ‐mediated buffering of acid‐base equivalents, they could not appreciably affect transport rates of NBCe1 or other transporters carrying HCO3− , CO3= , or NaCO3− ion pairs.
A Retrospective Study from 2 Centers in China on the Effects of Continued Use of Angiotensin-Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers in Patients with Hypertension and COVID-19

Background Use of renin-angiotensin-aldosterone system inhibitors in coronavirus disease 2019 (COVID-19) patients lacks evidence and is still controversial. This study was designed to investigate effects of angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) on clinical outcomes of COVID-19 patients and to assess the safety of ACEIs/ARBs medication. Material/Methods COVID-19 patients with hypertension from 2 hospitals in Wuhan, China, from 17 Feb to 18 Mar 2020 were retrospectively screened and grouped according to in-hospital medication. We performed 1: 1 propensity score matching (PSM) analysis to adjust for confounding factors. Results We included 210 patients and allocated them to ACEIs/ARBs (n=81; 46.91% males) or non-ACEIs/ARBs (n=129; 48.06% males) groups. The median age was 68 [interquartile range (IQR) 61.5–76] and 66 (IQR 59–72.5) years, respectively. General comparison showed mortality in the ACEIs/ARBs group was higher (8.64% vs. 3.88%) but the difference was not significant (P=0.148). ACEIs/ARBs was associated with significantly more cases 7-categorical ordinal scale >2 at discharge, more cases requiring Intensive Care Unit (ICU) stay, and increased values and ratio of days that blood pressure (BP) was above normal range (P<0.05). PSM analysis showed no significant difference in mortality, cumulative survival rate, or other clinical outcomes such as length of in-hospital/ICU stay, BP fluctuations, or ratio of adverse events between groups after adjustment for confounding parameters on admission. Conclusions We found no association between ACEIs/ARBs and clinical outcomes or adverse events, thus indicating no evidence for discontinuing use of ACEIs/ARBs in the COVID-19 pandemic.
Gastrointestinal Complications in Critically Ill Patients With and Without COVID-19.

Coronavirus disease 2019 (COVID-19) appears to have significant extrapulmonary complications affecting multiple organ systems.1-3 Critically ill patients with COVID-19 often develop gastrointestinal complications during their hospital stay, including bowel ischemia, transaminitis, gastrointestinal bleeding, pancreatitis, Ogilvie syndrome, and severe ileus.3 Whether the high incidence of gastrointestinal complications is a manifestation of critical illness in general or is specific to COVID-19 remains unclear. We compared the incidence of gastrointestinal complications of critically ill patients with COVID-19–induced acute respiratory distress syndrome (ARDS) vs comparably ill patients with non–COVID-19 ARDS using propensity score analysis.
A novel role for the pineal gland: Regulating seasonal shifts in the gut microbiota of Siberian hamsters

The gut microbiota plays a significant role in a variety of host behavioral and physiological processes. The mechanisms by which the gut microbiota and the host communicate are not fully resolved but include both humoral and direct neural signals. The composition of the microbiota is affected by internal (host) factors and external (environmental) factors. One such signal is photoperiod, which is represented endogenously by nocturnal pineal melatonin (MEL) secretion. Removal of the MEL signal via pinealectomy abolishes many seasonal responses to photoperiod. In Siberian hamsters (Phodopus sungorus), MEL drives robust seasonal shifts in physiology and behavior, such as immunity, stress, body mass, and aggression. While the profile of the gut microbiota also changes by season, it is unclear whether these changes are driven by pineal signals. We hypothesized that the pineal gland mediates seasonal alterations in the composition of the gut microbiota. To test this, we placed pinealectomized and intact hamsters into long or short photoperiods for 8 weeks, collected weekly fecal samples, and measured weekly food intake, testis volume, and body mass. We determined microbiota composition using 16S rRNA sequencing (Illumina MiSeq). We found significant effects of treatment and time on the abundances of numerous bacterial genera. We also found significant associations between individual OTU abundances and body mass, testis mass, and food intake, respectively. Finally, results indicate a relationship between overall community structure, and body and testis masses. These results firmly establish a role for the pineal gland in mediating seasonal alterations in the gut microbiota. Further, these results identify a novel neuroendocrine pathway by which a host regulates seasonal shifts in gut community composition, and indicates a relationship between seasonal changes in the gut microbiota and seasonal physiological adjustments.
Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
Man as an Intertidal Predator in Transkei: Disturbance, Community Convergence and Management of a Natural Food Resource

The indigenous peoples of Transkei, South Africa, remove shellfish from the shore to supplement their diet. Paired exploited and protected rocky shores were compared in terms of community structure and of the size structures of component species. Relative abundance of algae and sessile, inedible invertebrates is greater, and modal and mean sizes of exploited species are smaller at exploited sites than at protected sites. Disturbance through selective predation increases species richness, in line with the "intermediate disturbance hypothesis", and also leads to community convergence towards a common state. The recovery potential of these systems is high and the resource could best be managed on a "rotational cropping" basis.