Miracle-dz/UniFAR-FTUs huggingface dataset:
Metastatic melanoma causing small intestinal perforation at the jejunojejunostomy after Roux-en-Y gastric bypass: a case report

Abstract Background Metastatic melanoma of the small intestine is relatively common, and among affected patients, the proportion with involvement of the small intestine ranges from 35% to 70%. Small intestinal perforation as a primary manifestation of metastatic melanoma is rare. We present the exceptional case of a perforation at the jejunojejunostomy after Roux-en-Y gastric bypass caused by metastatic melanoma. Case presentation A 59-year-old woman with a history of a laparoscopic Roux-en-Y gastric bypass and toe amputation due to malignant melanoma (stadium IIIC) presented with an acute abdomen. The abdominal computed tomography scan showed a covered perforation at the jejunojejunostomy of the gastric bypass. The patient underwent an urgent surgical exploration revealing massive tumoral invasion of the anastomosis. The tumoral mass and anastomosis were resected and a new jejunojejunostomy was created. Histopathological examination identified the tumor as a malignant melanoma, so the current abdominal lesions were presumed to be metastases. The postoperative course was uneventful and adjuvant immunotherapy was started a week later. One year after surgery she was doing well with maintenance immunotherapy and there was no evidence of recurrent metastatic disease. Conclusion We report the first case of a perforation at the jejunojejunostomy after Roux-en-Y gastric bypass caused by metastatic melanoma. This exceptional case illustrates that a history of malignant melanoma in case of an acute abdomen should raise suspicion of possible metastatic disease.
Impact of red blood cell lysing on rare event analysis

The challenges associated with analyzing rare cells are dependent on a series of factors, which usually require large numbers of cells per sample for successful resolution. Among these is determining the minimum number of total events needed to be acquired as defined by the expected frequency of the target cell population. The choice of markers that identify the target population, as well as the event rate and the number of aborted events/second, will also determine the statistically significant detection of rare cell events. Sample preparation is another important but often overlooked factor in rare cell analysis, and in this study we examine Poisson theory and methods to determine the effect of sample manipulation on rare cell detection. After verifying the applicability of this theory, we have evaluated the potential impact of red cell lysis on rare cell analysis, and how cell rarity can be underestimated or overestimated based on erythrolytic sensitivity or resistance of healthy leukocytes and pathological rare cells.
Single cell RNA‐sequencing: A powerful yet still challenging technology to study cellular heterogeneity

Almost all biomedical research to date has relied upon mean measurements from cell populations, however it is well established that what it is observed at this macroscopic level can be the result of many interactions of several different single cells. Thus, the observable macroscopic ‘average’ cannot outright be used as representative of the ‘average cell’. Rather, it is the resulting emerging behaviour of the actions and interactions of many different cells. Single‐cell RNA sequencing (scRNA‐Seq) enables the comparison of the transcriptomes of individual cells. This provides high‐resolution maps of the dynamic cellular programmes allowing us to answer fundamental biological questions on their function and evolution. It also allows to address medical questions such as the role of rare cell populations contributing to disease progression and therapeutic resistance. Furthermore, it provides an understanding of context‐specific dependencies, namely the behaviour and function that a cell has in a specific context, which can be crucial to understand some complex diseases, such as diabetes, cardiovascular disease and cancer. Here, we provide an overview of scRNA‐Seq, including a comparative review of emerging technologies and computational pipelines. We discuss the current and emerging applications and focus on tumour heterogeneity a clear example of how scRNA‐Seq can provide new understanding of a complex disease. Additionally, we review the limitations and highlight the need of powerful computational pipelines and reproducible protocols for the broader acceptance of this technique in basic and clinical research.
Cytology of malignant pleural mesothelioma: Diagnostic criteria, WHO classification updates, and immunohistochemical staining markers diagnostic value

Malignant pleural mesothelioma (MPM) is a rare but aggressive malignancy with a poor prognosis. Because of this tumor rarity and overlapping histologic features with other malignancy types, the histopathological findings and diagnostic immunohistochemical workup are essential in establishing the final diagnosis of MPMs. We aimed to review the diagnostic criteria, WHO tumor classification updates, and immunohistochemical staining markers diagnostic value to achieve an appropriate clinical diagnosis.
Multispecies coexistence in fragmented landscapes

Significance The maintenance of biodiversity is a central theme in ecology and conservation biology. Although spatial dynamics have long been documented to influence biodiversity, coexistence theory has so far mainly focused on local communities. This not only limits the understanding of species coexistence to a single-site perspective but also largely restricts our ability to predict the impacts of habitat destruction. Here, we develop a spatially explicit competition model and derive analytical criteria for multispecies coexistence under realistic landscape configurations. By parameterizing our model using a long-term dataset of three Daphnia species in a rockpool metacommunity, we predict its possible responses to habitat destruction and temperature change. Our study provides theoretical and empirical platforms to understand multispecies coexistence in fragmented landscapes.
Zero-Shot Learning With Attentive Region Embedding and Enhanced Semantics

The performance of zero-shot learning (ZSL) can be improved progressively by learning better features and generating pseudosamples for unseen classes. Existing ZSL works typically learn feature extractors and generators independently, which may shift the unseen samples away from their real distribution and suffers from the domain bias problem. In this article, to tackle this challenge, we propose a variational autoencoder (VAE)-based framework, that is, joint Attentive Region Embedding with Enhanced Semantics (AREES), which is tailored to advance the zero-shot recognition. Specifically, AREES is end-to-end trainable and consists of three network branches: 1) attentive region embedding is used to learn the semantic-guided visual features by the attention mechanism (AM); 2) a decomposition structure and a semantic pivot regularization are used to extract enhanced semantics; and 3) a multimodal VAE (mVAE) with the cross-reconstruction loss and the distribution alignment loss is used to obtain a shared latent embedding space of visual features and semantics. Finally, features’ extraction and features’ generation are optimized together in AREES to address the domain shift problem to a large extent. The comprehensive evaluations on six benchmarks, including the ImageNet, demonstrate the superiority of the proposed model over its state-of-the-art counterparts.
CFD Simulation of Flow through Packed Beds using the Finite Volume Technique

When a disordered packed bed, or any heterogeneous media is studied using computational fluid dynamics, the tortuous task of generating a domain and creating a workable mesh presents a challenging issue to Engineers and Scientists. In this Thesis these challenges are addressed in the form of three studies in which both traditional and novel techniques are used to generate packed beds of spheres and cylinders for analysis using computational fluid dynamics, more specifically, the finite volume method. The first study uses a Monte-Carlo method to generate random particle locations for use with a traditional CADbased meshing approach. Computational studies are performed and compared in detail with experimental equivalent beds. In the second study, where there is a need for actual, physical beds to be studied, magnetic-resonance-imaging is used coupled with a novel approach known as image based meshing. In parallel experimental studies are performed on the experimental bed and compared with computational data. In the third study, to overcome fidelity issues with the previous approaches, a physical packed bed is manufactured which is 100% geometrically faithful to its computational counterpart to provide a direct comparison. All three computational studies have shown promising results in comparison with the experimental data described in this Thesis, with the data of Reichelt (1972) and the semi-empirical correlation of Eisfeld & Schnitzlein (2001). All experiments and computational models were carried out by the author unless otherwise stated.
1 Hydrogen Pseudopotential and Basis Sets

A significantly improved hydrogen pseudopotential developed by Filippi and Dolg is provided in Table 1. The s contraction for the hydrogen basis sets is given in Table 2. The Gauss-Slater (GS) primitives for the double-zeta (2z) atomic natural orbital GS (ANO-GS) basis for hydrogen are provided in Table 3. The GS primitives for the triple-zeta (3z) ANO-GS basis for hydrogen are provided in Table 4. The Gaussian primitives for the quintuple-zeta (5z) Gaussian basis for hydrogen are provided in Table 5. Each basis was constructed using the methods of Ref. [1].
Prosocial spending encourages happiness: A replication of the only experiment reported in Dunn, Aknin, and Norton (2008)

Spending money on one’s self, whether to solve a problem, fulfill a need, or increase enjoyment, often heightens one’s sense of happiness. It is therefore both surprising and important that people can be even happier after spending money on someone else. We conducted a close replication of a key experiment from Dunn, Aknin, and Norton (2008) to verify and expand upon their findings. Participants were given money and randomly assigned to either spend it on themselves or on someone else. Although the original study (N = 46) found that the latter group was happier, when we used the same analysis in our replication (N = 133), we did not observe a significant difference. However, we report an additional analysis, focused on a more direct measure of happiness, that does show a significant effect in the direction of the original. Follow-up analyses shed new insights into people’s predictions about their own and others’ happiness and their actual happiness when spending money for themselves or others.
Sacubitril/valsartan: An antiarrhythmic drug?

Heart failure (HF) is a major cause of morbidity and mortality, with nearly half of all HF‐related deaths resulting from sudden cardiac death (SCD), most often from an arrhythmic event. The pathophysiologic changes that occur in response to the hemodynamic stress of HF may lead to increased arrhythmogenesis. Theoretically, medications that block these arrhythmogenic substrates would decrease the risk of SCD. The combined angiotensin receptor and neprilysin inhibitor (ARNi; tradename Entresto) is the newest commercially available medication for the treatment of heart failure.
Serum levels of iCAF‐derived osteoglycin predict favorable outcome in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant stroma, the main cellular constituents of which are cancer‐associated fibroblasts (CAFs). Stroma‐targeting agents have been proposed to improve the poor outcome of current treatments. However, clinical trials using these agents showed disappointing results. Heterogeneity in the PDAC CAF population was recently delineated demonstrating that both tumor‐promoting and tumor‐suppressive activities co‐exist in the stroma. Here, we aimed to identify biomarkers for the CAF population that contribute to a favorable outcome. RNA‐sequencing reads from patient‐derived xenografts (PDXs) were mapped to the human and mouse genome to allocate the expression of genes to the tumor or stroma. Survival meta‐analysis for stromal genes was performed and applied to human protein atlas data to identify circulating biomarkers. The candidate protein was perturbed in co‐cultures and assessed in existing and novel single‐cell gene expression analysis from control, pancreatitis, pancreatitis‐recovered and PDAC mouse models. Serum levels of the candidate biomarker were measured in two independent cohorts totaling 148 PDAC patients and related them to overall survival. Osteoglycin (OGN) was identified as a candidate serum prognostic marker. Single‐cell analysis indicated that Ogn is derived from a subgroup of inflammatory CAFs. Ogn‐expressing fibroblasts are distinct from resident healthy pancreatic stellate cells and arise during pancreatitis. Serum OGN levels were prognostic for favorable overall survival in two independent PDAC cohorts (HR = 0.47, P = .042 and HR = 0.53, P = .006). Altogether, we conclude that high circulating OGN levels inform on a previously unrecognized subgroup of CAFs and predict favorable outcomes in resectable PDAC.
Assessment of thrombus using susceptibility‐weighted filtered‐phase images in patients with acute ischemic stroke

Recognizing the location and length of the thrombus responsible for large vessel occlusion in patients with acute ischemic stroke can facilitate effective endovascular recanalization therapy (ERT). We hypothesized that the aliasing or dipole effect produced by filtered‐phase susceptibility‐weighted imaging (SWI) would facilitate thrombus delineation.
Real-time Tracking and Classification of Tumor and Nontumor Tissue in Upper Gastrointestinal Cancers Using Diffuse Reflectance Spectroscopy for Resection Margin Assessment

Key Points Question Can the development of a diffuse reflectance spectroscopy (DRS) probe aid cancer margin assessment in esophageal and gastric cancer surgery? Findings In this validation study including 37 patients, the development of a DRS probe and tracking system showed that machine learning can provide real-time discrimination of normal and cancer tissue with high diagnostic accuracy of 93.9% and 96.2% for gastric and esophageal specimens, respectively. Meaning This study highlights the potential for the DRS system to be used intraoperatively to aid cancer margin assessment in real time.
Adaptation and Evolution of Pathogens in the Cystic Fibrosis Lung

Abstract As opposed to acute respiratory infections, the persistent bacterial infections of the lung that characterize cystic fibrosis (CF) provide ample time for bacteria to evolve and adapt. The process of adaptation is recorded in mutations that accumulate over time in the genomes of the infecting bacteria. Some of these mutations lead to obvious phenotypic differences such as antibiotic resistance or the well-known mucoid phenotype of Pseudomonas aeruginosa. Other mutations may be just as important but harder to detect such as increased mutation rates, cell surface changes, and shifts in metabolism and nutrient acquisition. Remarkably, many of the adaptations occur again and again in different patients, signaling that bacteria are adapting to solve specific challenges in the CF respiratory tract. This parallel evolution even extends across distinct bacterial species. This review addresses the bacterial systems that are known to change in long-term CF infections with a special emphasis on cross-species comparisons. Consideration is given to how adaptation may impact health in CF, and the possible evolutionary mechanisms that lead to the repeated parallel adaptations.
Insomnia symptoms and risk of bloodstream infections: prospective data from the prospective population‐based Nord‐Trøndelag Health Study (HUNT), Norway

Previous research suggests decreased immune function and increased risk of infections in individuals with insomnia. We examined the effect of insomnia symptoms on risk of bloodstream infections (BSIs) and BSI‐related mortality in a population‐based prospective study. A total of 53,536 participants in the second Norwegian Nord‐Trøndelag Health Study (HUNT2) (1995–97) were linked to prospective data on clinically relevant BSIs until 2011. In Cox regression, we estimated hazard ratios (HRs) with 95% confidence intervals (CIs) for a first‐time BSI and for BSI‐related mortality (BSI registered ≤30 days prior to death) associated with insomnia symptoms. Compared with participants who reported “no symptoms”, participants reporting having “difficulty initiating sleep” (DIS) often/almost every night had a HR for a first‐time BSI of 1.14 (95% CI 0.96–1.34). Participants reporting “difficulties maintaining sleep” (DMS) often/almost every night had a HR of 1.19 (95% CI 1.01–1.40), whereas those having a feeling of “non‐restorative sleep” once a week or more had a HR of 1.23 (95% CI 1.04–1.46). Participants frequently experiencing all three of the above symptoms had a HR of 1.39 (1.04–1.87), whilst those who had both DIS and DMS had a HR of 1.15 (0.93–1.41) and being troubled by insomnia symptoms to a degree that affected work performance was associated with a HR of 1.41 (95% CI 1.08–1.84). The HRs for BSI‐related mortality suggest an increased risk with increasing insomnia symptoms, but the CIs are wide and inconclusive. We found that frequent insomnia symptoms and insomnia symptoms that affected work performance were associated with a weak positive increased risk of BSI.
Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan

Plasmids are known to spread among different bacteria. However, which plasmids spread among environmental samples and in which environments they are present is still poorly understood. ABSTRACT Various conjugative plasmids were obtained by exogenous plasmid capture, biparental mating, and/or triparental mating methods from different environmental samples in Japan. Based on phylogenetic analyses of their whole-nucleotide sequences, new IncP/P-1 plasmids that could be classified into novel subgroups were obtained. Mini-replicons of the plasmids were constructed, and each of them was incompatible with at least one of the IncP/P-1 plasmids, although they showed diverse iteron sequences in their oriV regions. There were two large clades of IncP/P-1 plasmids, clade I and II. Plasmids in clade I and II included antibiotic resistance genes. Notably, nucleotide compositions of newly found plasmids exhibited different tendencies compared with those of the previously well-studied IncP/P-1 plasmids. Indeed, the host range of plasmids of clade II was different from that of clade I. Although few PromA plasmids have been reported, the number of plasmids belonging to PromAβ, and -γ subgroups detected in this study was close to that of IncP/P-1 plasmids. The host ranges of PromAγ and PromAδ plasmids were broad and transferred to different and distinct classes of Proteobacteria. Interestingly, PromA plasmids and many IncP/P-1 plasmids do not carry any accessory genes. These findings indicate the presence of “hitherto-unnoticed” conjugative plasmids, including IncP/P-1 or PromA derivative ones in nature. These plasmids would have important roles in the exchange of various genes, including antibiotic resistance genes, among different bacteria in nature. IMPORTANCE Plasmids are known to spread among different bacteria. However, which plasmids spread among environmental samples and in which environments they are present is still poorly understood. This study showed that unidentified conjugative plasmids were present in various environments. Different novel IncP/P-1 plasmids were found, whose host ranges were different from those of known plasmids, showing wide diversity of IncP/P-1 plasmids. PromA plasmids, exhibiting a broad host range, were diversified into several subgroups and widely distributed in varied environments. These findings are important for understanding how bacteria naturally exchange their genes, including antibiotic resistance genes, a growing threat to human health worldwide.
The pale spear‐nosed bat: A neuromolecular and transgenic model for vocal learning

Vocal learning, the ability to produce modified vocalizations via learning from acoustic signals, is a key trait in the evolution of speech. While extensively studied in songbirds, mammalian models for vocal learning are rare. Bats present a promising study system given their gregarious natures, small size, and the ability of some species to be maintained in captive colonies. We utilize the pale spear‐nosed bat (Phyllostomus discolor) and report advances in establishing this species as a tractable model for understanding vocal learning. We have taken an interdisciplinary approach, aiming to provide an integrated understanding across genomics (Part I), neurobiology (Part II), and transgenics (Part III). In Part I, we generated new, high‐quality genome annotations of coding genes and noncoding microRNAs to facilitate functional and evolutionary studies. In Part II, we traced connections between auditory‐related brain regions and reported neuroimaging to explore the structure of the brain and gene expression patterns to highlight brain regions. In Part III, we created the first successful transgenic bats by manipulating the expression of FoxP2, a speech‐related gene. These interdisciplinary approaches are facilitating a mechanistic and evolutionary understanding of mammalian vocal learning and can also contribute to other areas of investigation that utilize P. discolor or bats as study species.
The prognostic value of lymph node staging with prostate‐specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) and extended pelvic lymph node dissection in node‐positive patients with prostate cancer

To investigate whether patients with suspected pelvic lymph node metastases (molecular imaging [mi] N1) on staging prostate‐specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) had a different oncological outcome compared to those in whom the PSMA PET/CT did not reveal any pelvic lymph node metastases (miN0).
Tear instability in the fellow eye of unilateral nasolacrimal obstruction and resolution with dacryocystorhinostomy

ABSTRACT Purpose To determine the effect of unilateral primary acquired nasolacrimal obstruction (PANDO) on ocular surface parameters in PANDOeyes and fellow eyes and changes in these parameters after dacryocystorhinostomy. Methods Tear osmolarity, tear break-up time (TBUT), Schirmer’s test, Meibomian gland score, and Lissamine Green staining of PANDO eyes and fellow eyes were measured preoperatively and postoperatively at Day 15, 1 month, and 3 months. Lacrimal irrigation and epiphora symptomatology were evaluated at all follow-up visits, and patients who did not meet surgical success criteria were excluded from the study. Results Twenty-nine patients who underwent successful dacryocystorhinostomy surgery were included in the study. Preoperative and postoperative Day 15 Schirmer (p = .019, p = .001) and TBUT (p = .039, p = .043) were significantly lower in the fellow eye compared to PANDO eyes. The differences observed between PANDO eyes and fellow eyes in all other parameters were not significant (p > .05). Preoperatively PANDO eye parameters were normal, whereas TBUT (7.59 ± 5.39 s) and tear osmolarity (308.59 ± 17.32 mOsm/L) values of the fellow eye may be indicative of tear film instability. TBUT and tear osmolarity of the fellow eye showed significant improvement 3 months postoperatively compared to preoperative values (p = .010; p = .027 respectively). Conclusion Schirmer and TBUT values of the fellow eye were significantly lower than PANDO eyes preoperatively, one month after surgery there was no significant difference. TBUT and tear osmolarity of the fellow eyes may be indicative of tear instability preoperatively with improvement 3 months after dacryocystorhinostomy.