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Abstract A research protocol is a document that outlines the proposed research idea and is submitted to funding agencies, institutions, or journals for approval. Writing a research protocol represents a challenge, particularly for early-career researchers. In this guide, we aim to provide detailed guidance with the key components and offer practical tips for crafting a research protocol in line with the various study designs. Specifically, the structure of a research protocol should contain the following items: (1) a title that is specific, catchy, and impressive within the word limitation; (2) an abstract that briefs the critical points of the study; (3) an introduction highlighting the study context from broad to narrow and defining the knowledge gap; (4) a justification underlining the significance of the proposed study; (5) Specific, Measurable, Attainable, Relevant, and Time-bound (SMART) objective(s) and aim(s); (6) a methodology covering seven sub-items, including [i] study design and settings, [ii] study subjects, [iii] sample size calculation and sampling, [iv] participants recruitment and follow-up, [v] questionnaire development, [vi] potential variables and outcomes, and [vii] data analysis plan; (7) dissemination of the results; (8) ethics and conflict of interests; (9) budgets analysis/ funding disclosure; and (10) references. This guide will give an overview of these steps and provide clear and concise tips on how to successfully draft a scientific protocol. With careful planning and appropriate guidance, it is possible to develop a well-structured and compelling protocol to obtain approval for the conduction of the study or funding from agencies, institutions, or organizations.

Intravenous misplacement of the nephrostomy catheter following percutaneous nephrolithotomy (PCNL) is severe and extremely rare, and little information is available about this complication. Because the patient's prognosis may be poor, sufficient attention should be paid to early identification and treatment of this complication. We report a case with intravenous misplacement of nephrostomy catheter and severe bleeding from the catheter after PCNL was transferred to our hospital. The patient was successfully managed using a two-step intervention. First, the patient underwent embolization of the pseudoaneurysms in renal parenchyma, then underwent catheter withdrawal under digital subtraction angiography (DSA) and control bleeding by pushing the absorbable hemostatic material (Surgicel) into the tunneled renal drainage. There were no severe complications. Withdrawal could be performed by open surgery or under the supervision of imaging modalities. Some reports showed that minimally invasive management was safer and less invasive than open surgery.

In May 2022, the world witnessed the re-emergence of the zoonotic disease monkeypox. While this was not the first epidemic of this disease, what differentiated the outbreak was the rapid global spread and increase of cases, which led the WHO to declare monkeypox a global health emergency. Although the disease spreads mainly through inadequately cooked meat of various rodent species, this virus also shows droplet, respiratory, sexual, and even vertical transmission. Monkeypox further multiplies in lymphoproliferative organs and presents with a classical smallpox-like rash, fever, headache, and muscle aches. Diagnosis is confirmed with a polymerase-chain-reaction test and is managed largely supportively with possible usage of some antivirals and immunoglobulins. Moreover, some pre-exposure and postexposure prophylactic vaccines have been developed. This paper aims to conduct an in-depth review of the historical epidemics, transmission, pathophysiology, clinical presentation, and management of the monkeypox disease.

Cardiac cysticercosis is rare in clinical practice and is usually accidentally identified during cardiac surgery or autopsies. Although mostly asymptomatic, cardiac cysticercosis could present with severe clinical conditions such as myocarditis, acute myocardial infarction, and arrhythmia. We present a 51-year-old female patient who accidentally discovered a solitary mass in the myocardium. The cardiac magnetic resonance imaging revealed a nonenhanced cyst in the interventricular septum protruding into the right ventricular chamber. Because of cardiac tamponade presenting during a right ventricular endomyocardial biopsy, an emergency open-heart surgery was performed to suture the ventricular wall perforation and remove the tumor. The histopathologic report demonstrated typical cysticercosis. Cardiac cysticercosis is an uncommon lesion and may present with atypical clinical and laboratory features. Therefore, this diagnosis should be considered single or multiple cardiac cystic lesions.

Phlebosclerotic colitis (PC), also known as idiopathic mesenteric phlebosclerosis, is a rare disease resulting in ischemic colon due to venous sclerosis and calcifications that can be identified by characteristic imaging features on computed tomography and colonoscopy. Clinical examination reveals nonspecific symptoms with slow progression in the majority of cases. Patients with PC often require late-stage hospitalization and colectomy. We report a 79-year-old man with long-term clinical symptoms who used herbal medicines. Computed tomography and colonoscopy studies revealed several classical PC characteristics, and the patient subsequently underwent emergency total colectomy.

Chordoid gliomas are uncommon neoplasms located within the anterior portion of the third ventricle. In this article, we aimed to describe the clinical presentation, magnetic resonance imaging characteristics, histological findings, and surgical treatment applied to a case of chordoid glioma. Chordoid gliomas are typically observed as solid masses within the anterior segment of the third ventricle, characterized by homogenous and vivid enhancement. Despite being classified as a low-grade neoplasm, the outcome of choroid glioma is often uncertain.

It is currently assumed that around 100 million years ago, the common ancestor to the Fabales, Fagales, Rosales and Cucurbitales in Gondwana, developed a root nodule symbiosis with a nitrogen-fixing bacterium. The symbiotic trait evolved first in Frankia cluster-2; thus, strains belonging to this cluster are the best extant representatives of this original symbiont. Most cluster-2 strains could not be cultured to date, except for Frankia coriariae, and therefore many aspects of the symbiosis are still elusive. Based on phylogenetics of cluster-2 metagenome-assembled genomes (MAGs), it has been shown that the genomes of strains originating in Eurasia are highly conserved. These MAGs are more closely related to Frankia cluster-2 in North America than to the single genome available thus far from the southern hemisphere, i.e., from Papua New Guinea.To unravel more biodiversity within Frankia cluster-2 and predict routes of dispersal from Gondwana, we sequenced and analysed the MAGs of Frankia cluster-2 from Coriaria japonica and Coriaria intermedia growing in Japan, Taiwan and the Philippines. Phylogenetic analyses indicate there is a clear split within Frankia cluster-2, separating a continental from an island lineage. Presumably, these lineages already diverged in Gondwana.Based on fossil data on the host plants, we propose that these two lineages dispersed via at least two routes. While the continental lineage reached Eurasia together with their host plants via the Indian subcontinent, the island lineage spread towards Japan with an unknown host plant.

Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.

Background: Xuan Lien Nature Reserve was established in 1999 to protect important habitats and wildlife in the northern part of the Annamites in Vietnam. While Xuan Lien is home to many threatened species, it has experienced a high level of human disturbance over the last decades. To document and provide baseline data on the status and distribution of the terrestrial vertebrate fauna community in the region, we conducted a systematic camera trapping survey in Xuan Lien Nature Reserve in 2023. The data collected during the survey will help design proper conservation measures to better conserve the remaining species. New information: Our study investigates and updates the species richness of mid- to large-sized terrestrial vertebrates, thus providing essential information for developing conservation strategies in Xuan Lien Nature Reserve, Vietnam. As camera traps were set up in a grid-based design, our survey also generated the first-ever systematic data for terrestrial vertebrate fauna in the area. The study covers approximately 21,000 hectares (about 77% of the area), using 35 camera trap stations; each station consists of two cameras. In total, the final dataset consists of 6,276 trap nights, recording at least 46 species in 39 genera. The results suggest that Xuan Lien is a key stronghold for small carnivores, based on the diversity of such species groups in the Reserve. We failed to detect the previously documented Roosevelt's muntjac (Muntiacus rooseveltorum Osgood, 1932) and we only documented a single record of the northern red muntjac (Muntiacus vaginalis Boddaert, 1785). Our survey confirms the severity of overhunting and other anthropogenic threats to the mammal fauna, especially ungulates, in the Reserve. [ABSTRACT FROM AUTHOR]

Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.

BackgroundThe ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically, Frankia strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents. Two Cluster II genomes were sequenced thus far, both from Asia.ResultsIn this paper we present the first Frankia cluster II genome from North America (California), Dg2, which represents a metagenome of two major and one minor strains. A phylogenetic analysis of the core genomes of 16 Frankia strains shows that Cluster II the ancestral group in the genus, also ancestral to the non-symbiotic Cluster IV. Dg2 contains the canonical nod genes nodABC for the production of lipochitooligosaccharide Nod factors, but also two copies of the sulfotransferase gene nodH. In rhizobial systems, sulfation of Nod factors affects their host specificity and their stability.ConclusionsA comparison with the nod gene region of the previously sequenced Dg1 genome from a Cluster II strain from Pakistan shows that the common ancestor of both strains should have contained nodABC and nodH. Phylogenetically, Dg2 NodH proteins are sister to rhizobial NodH proteins. A glnA-based phylogenetic analysis of all Cluster II strains sampled thus far supports the hypothesis that Cluster II Frankia strains came to North America with Datisca glomerata following the Madrean-Tethyan pattern.

Background: The B-type rafkinase (BRAF) V600E gene mutation plays an important role in the pathogenesis, diagnosis, and prognosis of thyroid carcinoma. This study was conducted to investigate the rate of the BRAF V600E mutation, the relationships between the BRAF V600E gene mutation and some immunohistochemical markers, and recurrence rate in patients with differentiated thyroid cancer. Method: The study was conducted by a descriptive and longitudinal follow-up method on 102 thyroid carcinoma patients at 103 Military Hospital, Hanoi, Vietnam. All patients were identified with the BRAF V600E gene mutation by real-time polymerase chain reaction. Results: The rate of BRAF V600E gene mutation in patients with thyroid cancer was 60.8%. Patients with BRAF V600E gene mutation had a significantly higher rate of positive cyclooxygenase 2 (COX-2) and Ki67 markers than those without the mutation (COX-2: odds ratio [OR] = 2.93; 95% confidence interval [CI] = 1.27-6.74, P =.011; Ki67: OR = 3.41; 95% CI = 1.31-8.88, P =.01). A statistically significant relationship was identified between the rate of BRAF V600E mutation and the rate of positive Hector Battifora mesothelial 1 (HBME-1) (B = −1.040; P =.037) and COX-2 (B = −1.123; P =.023) markers. The recurrence rate in patients with BRAF V600E gene mutation was significantly higher than that in those without the mutation (P =.007). The mean of the recurrence time of patients with BRAF V600E mutation was significantly lower than that in those without the mutation (P =.011). Conclusions: A high prevalence of BRAF V600E gene mutation was found in thyroid carcinoma patients. The rates of positive HBME-1, COX-2, and Ki67 markers were significantly correlated to BRAF V600E gene mutation. Patients with BRAF V600E gene mutation showed a significantly higher relapse rate and earlier relapse time than those without the mutation. [ABSTRACT FROM AUTHOR]

Background: Tacrolimus (Tac) has been widely used with other immunosuppressive agents to prevent graft rejection post-kidney transplantation. However, the usage of Tac has depended on experience rather than evidence-based methods. In the present study, the authors investigated the Tac usage patterns and outcomes in kidney-transplanted patients at a transplant center located in the North of Vietnam. Materials and Methods: A retrospective cross-sectional study was conducted. Patients were included if they underwent renal transplantation, received Tac as part of the immunosuppressive therapy, and had been followed up in Viet Duc Hospital during the period between February 2009 and February 2019. Excluded patients were those who did not use Tac or switched to another drug during treatment. Results: The number of followed up patients steadily decreased from 342 cases in the first six months to 281 cases in the second year, 217 in the third year, 185 in the fourth year, and 152 in the fifth year post-transplanted. Only 17 cases had a ten-year follow-up. The number of transplants from deceased donors at 9.6% was much lower than live donors at 90.4%. Three patients died through the five years of the follow-up due to causes unrelated to kidney transplantation. Ten cases were ABO-incompatible transplantations. The mean blood concentration of Tac was highest in the first six months with 10.6 ng/mL, then gradually dropped to the lowest value at 6.3 ng/mL in the fifth year. Seven cases were identified as graft rejection with no clear outcome. Conclusion: Although there were a lack of standard tests and facilities for taking care of kidney transplant patients, the intra-patient variability and Tac concentration of included patients in the author’s center were close to the international studies in developed countries in five years follow-up. [ABSTRACT FROM AUTHOR]