bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case report: A case of Paget disease outside the axillary breast
Authors: Zhou Zhibing , Zhou Bing , Wu Xiaobo , Wei Wensong 
Published: March 2024

Background:
Extramammary Paget disease is a relatively rare and less malignant intraepithelial adenocarcinoma. t is found in areas with abundant distribution of apocrine sweat glands such as the external genitalia, external genitalia, and perianal area, with fewer armpits. The disease progresses slowly and is prone to misdiagnosis in clinical practice.

Methods:
We retrospectively analyzed a female patient. She had a left axillary mass for more than 2 years. Recently, the mass increased and the surface skin was ulcerated. Then she went to Jiangxi Provincial Dermatology Hospital for left axillary lesion resection, and the postoperative pathology showed Paget disease outside the breast. For further diagnosis and treatment, she came to our hospital. We diagnosed a tumor with uncertain or unknown dynamics in the left axillary breast. Under general anesthesia, left subaxillary mass resection, freezing and left breast cancer breast conserving surgery was performed.

Results:
The postoperative pathology of the left axillary mass combined with morphological and immunohistochemical results was consistent with Paget disease. Postoperative immunohistochemistry showed estrogen receptor (+, 20%), progesterone receptor (−), human epidermal growth factor receptor-2 (3+), Ki-67 (30%), cytokine7 (+), and p63 (−). Following up for 22 months, there has been no local recurrence, no swelling of the right axillary lymph node, no distant metastasis found on follow-up, and no complications such as upper limb lymphedema, upper limb sensory abnormalities, or motor disorders have been observed.

Conclusion:
Paget disease outside the axillary breast is relatively rare, and surgical resection is the best choice. The prognosis is good, and the recurrence rate is low.
Severe hyponatremia and diabetes insipidus caused by low-dose cyclophosphamide in breast cancer patients: A case report and literature review
Authors: Chen Yanfang , Li Liye , Ou Ruilian , Wu Yulan , Pan Baoying , Luo Linying 
Published: March 2024

Rationale:
Cyclophosphamide (CTX) is widely used in the treatment of malignancies and autoimmune diseases. Although severe hyponatremia caused by low-dose CTX chemotherapy is uncommon, it can lead to serious complications and even death.

Patient concerns:
A 44-year-old woman with left-sided breast cancer suddenly experienced headaches, disorientation and weakness after receiving low-dose neoadjuvant chemotherapy combined with CTX and doxorubicin.

Diagnoses:
The patient pathology showed invasive breast carcinoma. She developed severe hyponatremia and a generalized seizure after completing the first cycle of neoadjuvant chemotherapy with CTX and doxorubicin. Laboratory tests showed a serum sodium of 118 mmol/L (normal range 135–145 mmol/L) and potassium sodium 3.16 mmol/L (normal range 3.5–5.5 mmol/L). Subsequently, the patient developed secondary diabetes insipidus 4 hours after sodium supplementation, her 24-hour urine volume was 4730 mL (normal range 1000–2000 mL/24 hours), and the urine specific gravity decreased to 1.005.

Interventions:
The patient was given intravenous sodium chloride (500 mL of 3%NaCl, 100 mL/hour) and potassium chloride (500 mL of 0.3%KCl, 250 mL/hour). Meanwhile, she was advised to reduce her water intake, and pituitrin was administered to prevent dehydration caused by diabetes insipidus.

Outcomes:
The patient completely recovered after correcting of the serum sodium concentration (137 mmol/L) without any neurological deficits. After discontinuing pituitrin, her 24-hour urine volume was 2060 mL and the urine specific gravity was 1.015.

Lessons:
This is a typical case of severe hyponatremia induced by low-dose CTX. Clinicians and healthcare providers should be aware of this potential toxicity, and appropriate monitoring should be implemented.
Challenging diagnosis of male intraductal papilloma masquerading as eccrine hidradenoma in the breast: Case report
Authors: Liu Xinyue , Du Jie , Zhao Lirong 
Published: March 2024

Rationale:
This article presents a challenging case involving an elderly male patient with a misdiagnosed intraductal mammary papilloma initially identified as a sweat adenoma through ultrasound imaging. The study aims to explore the histopathology, clinical presentations, and sonographic features of both conditions, emphasizing the contributing factors to the diagnostic misstep.

Patient Concerns:
A 61-year-old male reported a persistent left breast mass, along with pain and swelling, spanning a 6-month duration.

Diagnoses:
Ultrasound examination indicated a deep, square, mixed-echo mass in the left nipple, initially suggestive of a sweat adenoma. However, subsequent pathological analysis following resection under general anesthesia confirmed an intraductal papilloma.

Intervention:
The patient underwent surgical resection of the left breast mass under general anesthesia.

Outcome:
Post-surgery, the patient exhibited satisfactory recovery; however, regrettably, he was lost to follow-up.

Lessons:
This study underscores the challenge in differentiating between clear cell sweat adenoma and male intraductal mammary papilloma solely based on ultrasonic characteristics. It emphasizes the susceptibility of ultrasound-based diagnoses to misinterpretation, highlighting the critical need for a comprehensive pathological examination to establish a definitive diagnosis.
A 42-year-old patient with renal cell carcinoma presenting as low back pain: A case report
Authors: Shim Ga Yang , Kim Min-Su , Kim Hong Jun , Park Yewan , Kim So-Woon , Yoo Myung Chul 
Published: March 2024

Rationale:
Renal cell carcinoma (RCC) is the most common renal neoplasm, accounting for 2.4% of all cancers in Korea. Although the usual clinical manifestations of RCC include flank pain, hematuria, and palpable mass, RCC is generally characterized by a lack of early warning signs and is mostly discovered incidentally in advanced stage. This case report describes a 42-year-old Korean man diagnosed with giant RCC who presented with simple back pain.

Patient concerns:
The clinical manifestation of a 42-year-old Korean man was chronic back pain.

Diagnoses:
Contrast-enhanced computed tomography showed a 19.1-cm sized heterogeneous enhancing mass on the right kidney and tumor thrombosis extending into inferior vena cava.

Intervention:
Due to the large size of the tumor and extensive tumor thrombosis, the multidisciplinary team decided to administer neoadjuvant chemotherapy and an anticoagulant. Following 12 cycles of treatment with nivolumab and cabozantinib, he underwent a right radical nephrectomy with an adrenalectomy and tumor thrombectomy.

Outcomes:
Treatment was successful and posttreatment he started a cancer rehabilitation program. He was followed-up as an outpatient and no longer complains of back pain.

Lessons:
RCC can manifest clinically as back pain, with diagnosis being difficult without appropriate imaging modalities. RCC should be included in the differential diagnosis of patients with low back pain, even at a young age.
Initial experiences and troubleshooting of Senhance robotic system: A community hospital perspective
Authors: Lin Yen-Chun , Huang Yu-Wen , Huang Shi-Wei , Huang Chao-Yuan , Yuan Lun-Hsiang 
Published: March 2024

Purpose:
The purpose of this study is to demonstrate the feasibility and safety of the Senhance robotic system in urologic surgeries.

Materials and methods:
Patients were included prospectively from July 2018 to December 2020. The exclusion criteria included severe cardiopulmonary diseases and previous extensive abdominal surgeries. Institutional approval and informed consent were obtained. We used the Clavien-Dindo classification system to evaluate the complications that occurred within 30 days after surgery. Common technical and mechanical events encountered were also recorded.

Results:
A total of 173 patients were recruited. The median age was 65 (58–74) years, and the median body mass index was 24.7 (16.5–35.6) kg/m2. Seventeen (9.8%) patients had previously undergone abdominal surgeries. Eighty-three (48%) cases had total extraperitoneal hernioplasty and 32 (18.5%) cases radical prostatectomy, which were the largest 2 surgeries in our study. Sixty-one (35.3%) patients received surgeries due to malignancy. The median docking time was 5 (1–35) minutes. There were 28 (16.2%) cases with grade I complications and 9 (5.2%) cases with grade II complications. Only one case of a grade IIIb complication occurred during radical prostatectomy. No grade IV complications or mortalities were noted. Robotic arm collisions and forces exceeding the limit were the most commonly encountered problems intraoperatively.

Conclusion:
In our initial experiences, the Senhance robotic system was feasible in oncologic and nononcologic urologic surgeries and had acceptable outcomes. The haptic feedback system is unique and requires a learning period. This system may serve as an alternative tool for robotic urologic surgeries.
Allium ureteral stent for refractory ureteral stricture: A single-center study
Authors: Wu Yun-Rui , Chuang Te-Yen , Lai Yi-Horng , Wang Chung-Cheng 
Published: March 2024

Purpose:
This study aims to investigate the efficacy and safety of Allium metallic ureteral stents in treating patients with refractory ureteral strictures.

Materials and methods:
A total of 13 patients with refractory ureteral strictures were prospectively enrolled in the study. After ureteral balloon dilation, an Allium stent was inserted into the ureter through the stricture. Serum blood urea nitrogen and creatinine levels, kidney-ureter-bladder x-ray, and renal ultrasonography reports were evaluated preoperatively, 3 months after the procedure, and at the last outpatient visit. Treatment success was defined as improvement in both renal function and the grade of hydronephrosis. Improvement was defined as the enhancement of renal function without the resolution of hydronephrosis. Adverse events were recorded.

Results:
The median (interquartile range [IQR]) age of the patients was 63 (46–76) years. The median (IQR) follow-up was 15 (13.5–21) months. Treatment success and improvement were noted in 9 (69.2%) and 3 (23.1%) patients, respectively. Compared with the preoperative levels, the median (IQR) serum creatinine levels were significantly improved at 3 months after the operation (1.6 [1.25–2.85] versus 1.2 [1.05–2.05]; P = 0.02) and at the last visit (1.6 [1.25–2.85] versus 1.2 [1.05–1.8]; P = 0.02). Stent migration and encrustation were noted in 3 (23.1%) and 1 (7.7%) patients, respectively.

Conclusion:
Allium ureteral stents are safe and effective for patients with refractory ureteral strictures.
Identification of Aggregation Pheromone inOdontothrips loti(Thysanoptera: Thripidae)
Authors: Yanqi Liu , Ying Ning Luo , Chang Liu , Liping Ban 
Published: March 2024

AbstractPheromone trapping is an interspecific, active at low concentrations, eco-friendly pest management strategy that has been widely used for population monitoring. Pheromones have only been validated for a few species in Thysanoptera and the pheromone components ofOdontothrips lotiHaliday are still unclear. In our study, we have identified (R)-lavandulyl (R)-2-methylbutanoate from maleO. lotiheadspace volatiles by gas chromatography-mass spectrometry (GC-MS), which was structurally similar to the known reported aggregation pheromone ofMegalurothrips sjostedti. Y-tube olfactometer assays showed that both male and female adultsO. lotiwere significantly attracted by synthetic (R)-lavandulyl (R)-2-methylbutyrate, implicating as an aggregation pheromone. Additionally, electroantennogram responses ofO. lotiincreased with increasing doses of synthetic (R)-lavandulyl (R)-2-methylbutyrate. This is the first report of a male-produced aggregation pheromone inO. loti, from genusOdontothrips. The discovery of aggregation pheromone ofO. lotias a primary pest of alfalfa will provide the possibility of monitoring and early warning in alfalfa grass fields and is expected to be used for integrated management forO. loti.
Lapidary: Identifying and reporting amino acid sequences in metagenomes using sequence reads and Diamond
Authors: Bloomfield Samuel J , Zomer Aldert L , Mather Alison E 
Published: March 2024

AbstractGenome and metagenome comparisons rely on identifying genetic elements that differ or are in common between samples. These genetic elements can be identified by assembling sequenced reads and identifying the genetic element in the assembly, or by aligning nucleotide sequences in the reads to the nucleotide sequences of a reference genetic element. The first relies on the complete assembly of the genetic element of interest, and the second relies on a reference sequence represented in nucleotides. This is particularly challenging with metagenome data, where the genetic elements, including genes, are often fragmented because sequences are shared between different species in the metagenomic data, resulting in contig breaks in or around genetic elements. This presents a difficulty when identifying genetic elements through the first approach. A common approach with metagenomes is to map reads against reference nucleotide sequences and extract the depth and coverage from those reference sequences. However, currently no software exists to identity and report genetic elements using DNA-protein alignments in metagenomes. We have developed the software Lapidary to identify the identity, coverage, depth, and most likely sequence of amino acid sequences from both genome and metagenome read files. We tested the effectiveness of the method against simulated, genomic and metagenomic read datasets. Lapidary is more sensitive than assembly methods for metagenomic data that often have fragmented assemblies but is less sensitive when assemblies are more complete, as is the case with genomic data.
KIR3DL1 and Tox identify clonally expanded encephalitogenic neuron-specific CD8+ T cells in autoimmune encephalitis
Authors: Perriot Sylvain , Jones Samuel , Genolet Raphaël , Mathias Amandine , Lindsay Helen , Bobisse Sara , Liberto Giovanni Di , Canales Mathieu , Queiroz Lise , Sauvage Christophe , Wagner Ingrid , Oberholster Larise , Gimenez Marie , Bégarie Diane , Théaudin Marie , Pot Caroline , Merkler Doron , Gottardo Raphaël , Harari Alexandre , Pasquier Renaud Du 
Published: March 2024

AbstractAutoreactive CD8+ T cells are the principal suspects in autoimmune encephalitis (AIE) with antibodies targeting intracellular neuronal antigens So far, the search for neuron-autoreactive CD8+ T cells has been focused on a few autoantigens and did not yield convincing results. Here, we leveraged natural antigen presentation by hiPSC-derived neurons to look at the global autoreactive CD8+ T cell response, independently of pre-conceived hypothesis of the autoantigens involved in the disease. This unbiased approach allowed for the identification of rare polyclonal neuron-reactive CD8+ T cells in healthy donors, and contrastingly, expanded clonotypes in two patients with anti-Ri AIE. Detailedex vivophenotypic characterization of these clonotypes revealed a specific transcriptional program suggestive of a pathogenic potential. In particular, this subset can be identified by the expression of KIR3DL1 and TOX. Strikingly, we could also demonstrate that CD8+ T cells found in the brain of an anti-Ri AIE patient display a similar phenotype associated with cytotoxicity and encephalitogenic features.
Using absorbance detection for hs-SV-AUC characterization of adeno-association virus
Authors: Larson Nicholas R. , Bou-Assaf George M. , Laue Thomas M. , Berkowitz Steven A. 
Published: March 2024

AbstractData are presented demonstrating that absorbance detection can be used during high-speed sedimentation velocity analytical ultracentrifugation (hs-SV-AUC) experiments to accurately characterize adeno-associated virus (AAV) drug products. Advantages and limitations of being able to use this detector in this specific type of SV-AUC experiment are discussed.
Comparing Phoneme and Word Recognition Test Outcomes in Adult CI users: Data Analysis from the AuDieT Study
Authors: Migliorini Enrico , Wasmann Jan-Willem A. , Philpott Nikki , van Dijk Bastiaan , Philips Birgit , Huinck Wendy 
Published: March 2024

AbstractPurposeCurrent clinical measures used in cochlear implantation (CI) provide a broader view of speech recognition ability at word-level, often missing granular details contained at phoneme-level that may be valuable for CI mapping. This study evaluates how outcomes of Phoneme Recognition in Quiet tests (PRQ) differ from those of more commonly used word recognition tests (CVC) and outlines how these tests may be useful for different purposes in clinical adult CI care.MethodsAs part of the AuDiET (Auditory Diagnostics and Error-based Treatment) study, 23 adult postlingually deafened unilateral CI users underwent a battery of tests, including both PRQ and CVC tests. Their results were compared at the phoneme level, including an evaluation of fitness and error dispersion.ResultsPRQ had a significantly lower accuracy and fitness than CVC. The error patterns also tended to be less random and more systematic. Fitness correlated strongly and positively with accuracy, while error dispersion negatively correlated with accuracy.ConclusionThere are clear differences between PRQ and CVC outcomes in absolute accuracy and error distribution. Comparing these tests might provide clinicians with more granular insights into which areas/phonemes to target during mapping, to achieve optimal speech recognition.
Optimizing Contingency Management with Reinforcement Learning
Authors: Kim Young-geun , Brandt Laura , Cheung Ken , Nunes Edward V. , Roll John , Luo Sean X. , Liu Ying 
Published: March 2024

ABSTRACTContingency Management (CM) is a psychological treatment that aims to change behavior with financial incentives. In substance use disorders (SUDs), deployment of CM has been enriched by longstanding discussions around the cost-effectiveness of prized-based and voucher-based approaches. In prize-based CM, participants earn draws to win prizes, including small incentives to reduce costs, and the number of draws escalates depending on the duration of maintenance of abstinence. In voucher-based CM, participants receive a predetermined voucher amount based on specific substance test results. While both types have enhanced treatment outcomes, there is room for improvement in their cost-effectiveness: the voucher-based system requires enduring financial investment; the prize-based system might sacrifice efficacy. Previous work in computational psychiatry of SUDs typically employs frameworks wherein participants make decisions to maximize their expected compensation. In contrast, we developed new frameworks that clinical decision-makers choose actions, CM structures, to reinforce the substance abstinence behavior of participants. We consider the choice of the voucher or prize to be a sequential decision, where there are two pivotal parameters: the prize probability for each draw and the escalation rule determining the number of draws. Recent advancements in Reinforcement Learning, more specifically, in off-policy evaluation, afforded techniques to estimate outcomes for different CM decision scenarios from observed clinical trial data. We searched CM schemas that maximized treatment outcomes with budget constraints. Using this framework, we analyzed data from the Clinical Trials Network to construct unbiased estimators on the effects of new CM schemas. Our results indicated that the optimal CM schema would be to strengthen reinforcement rapidly in the middle of the treatment course. Our estimated optimal CM policy improved treatment outcomes by 32% while maintaining costs. Our methods and results have broad applications in future clinical trial planning and translational investigations on the neurobiological basis of SUDs.
The rise of cheats during experimental evolution is restricted by non-kin interactions betweenBacillus subtilissoil isolates
Authors: Pandur Katarina Belcijan , Kraigher Barbara , Tomac Ana , Stefanic Polonca , Mulec Ines Mandic 
Published: March 2024

ABSTRACTCooperative behaviors in human, animal, and even microbial societies are vulnerable to exploitation. Kin discrimination (KD) has been hypothesized to help stabilize cooperation. However, the mechanisms that sustain cooperative behavior remain poorly understood. We here investigate the role of KD in limiting the rise of cheats during surfactant dependent cooperative swarming over surfaces by bacteriumBacillus subtilisas a model organism. We show that mixing surfactant secreting cooperators and cheats that do not produce surfactants leads to cooperation collapse. However, when such mixed swarms transiently encounter non-kinB. subtilisswarms, the frequency of the surfactant nonproducers decreases, suggesting that kinship dependent interactions may limit cheats’ advantage. To further validate this hypothesis, we subjected wild-type co-operators to transient encounters with kin and non-kin swarms over 20 cycles of experimental evolution. Evolved populations exposed to non-kin swarms exhibited lower occurrences of genotypes with defective swarming phenotypes compared to those encountering kin swarms. These results provide compelling support for the prediction that the evolution of cheats in bacterial populations is impeded by kin discrimination providing experimental proof of its role in stabilizing cooperative behavior.
Guavacv.Allahabad Safeda Chromosome scale assembly and comparative genomics decodes breeders’ choice marker trait association for pink pulp colour
Authors: Mittal Amandeep , Thakur Sujata , Sharma Ankush , Boora Rajbir Singh , Arora Naresh Kumar , Singh Daljinder , Singh Gill Manav Indra , Dhillon Guriqbal Singh , Chhuneja Parveen , Yadav Inderjit Singh , Jindal Manish , Mathew Oommen K. , Reddy Lachagari Vijaya Bhasker , Paterson Andrew H. 
Published: March 2024

AbstractDeciphering chromosomal length genome assemblies has the potential to unravel an organism’s evolutionary relationships and genetic mapping of traits of commercial importance. We assembled guava genome using a hybrid sequencing approach with ∼450x depth Illumina short reads, ∼35x PacBio long reads and Bionano maps to ∼594 MB Scaffold length on 11 pseudo chromosomes (∼479 MB contig length). Maker pipeline predicted 17,395 genes, 23% greater from earlier draft produced in same cultivar Allahabad Safeda. The genome assembly clarified guava evolutionary history, for example revealing predominance of gene expansion by dispersed duplications, in particular contributing to abundance of monoterpene synthases; and supporting evidence of a whole genome duplication event in guava as in other Myrtaceae. Guava breeders have been aiming to reduce screening time for selecting pink pulp colour progenies using marker-trait associations, but a previous comparative transcriptomics and comparative genomics approach with draft genome assembly to identify the effector gene associated with pink pulp was unsuccessful. Here, genome re-sequencing with Illumina short reads at ∼25x depth of 20 pink fleshed and/or non-coloured guava cultivars and comprehensive analysis for genes in the carotenoid biosynthesis pathway identified structural variations inPhytoene Synthase2. Further, ddRAD based association mapping in core-collection of 82 coloured and non-coloured genotypes from Indian sub-continent found strong association with the same causal gene. Subsequently, we developed PCR based Indel/SSR breeder friendly marker that can readily be scored in routine agarose gels and empowers accurate selection for seedlings that will produce fruits with pink pulp.