Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth, mortality and exploitation of buccaneer anchovy (Encrasicholina punctifer Fowler, 1938) from the north Persian Gulf and Oman Sea

The population parameters of Encrasicholina punctifer (Buccaneer anchovy) from commercial fishery in the Persian Gulf and Oman Sea coastal waters were studied from October 2014 to September 2015. A total of 13951 length-frequency data collected monthly by pair-boat purse seine and beach seine methods. The asymptotic length (L∞) and Von Bertalanffy growth function (K) were 11.5 cm and K = 1.4 per year, respectively. The value of to was calculated as -0.14 year. The longevity estimated 2 years. The total length ranged from 2.9 to 10.1 cm, with average 6.5 cm. The probability of capture were calculated in total length as L25=6.05 cm, L50=6.48 cm and L75=6.93 cm. Four cohorts distinguished annually with mean length of 4.56, 5.77, 7.21 and 8.50 cm. The length-weight relationship was determined as W= 0.0051 L 3.1114. Total, natural and fishing mortality parameters were estimated, 6.15, 2.84 and 3.32 yr-1 respectively. The current rate of exploitation (E) was given as 0.54, the values of exploitation ratio was found reasonable for current fishing effort. From the yield-per-recruit analysis, Emax, was estimated as 0.91. The results indicated that the Buccaneer anchovy stock was not overexploited, since E
A case report

Rationale: Primary schwannoma of the thyroid gland is very rare, and its preoperative diagnosis is difficult. Patient concerns:We report the case of a thyroid nodule in an 18-year-old woman, who presented with a mass in her left neck with stiffness and normal thyroid function. However, the patient complained of numbness in her left upper extremity, and ultrasound (US) features were suspicious of malignancy. Diagnosis: Multimodal US imaging was performed using B-mode, color doppler, ultrasonic elastography (UE), and contrastenhanced ultrasound (CEUS). CEUS revealed heterogeneous enhancement and “target sign” within the tumor. The nodule was suspicious for malignancy and classified as TI-RADS 4b, while the elasticity values measured by UE indicated a benign lesion. Fine needle aspiration (FNA) was subsequently performed in themarkedly contrast-enhanced area for biopsy. Cytological results revealed a benign schwannoma. Intervention:The patient underwent left lobe resection. Postoperative pathology confirmed it to be a primary benign schwannoma of the thyroid. Outcome:After thyroidectomy, the patient was followed-upwith US. At present, all laboratory tests and thyroid imaging are normal, and the numbness of the left upper limb has disappeared. Lesson: The combination of different US modalities is useful for the diagnosis of thyroid lesions. FNA performed under CEUS guidance improves the accuracy of biopsy sampling.
JCB_201409058 1..14

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 208 No. 4 415–428 www.jcb. org/cgi/doi/10.1083/jcb.201409058 JCB 415 *A. Fennell and A. Fernández-Álvarez contributed equally to this paper. Correspondence to Julia Promisel Cooper: julie.cooper@nih.gov Abbreviations used in this paper: GBP, GFP-binding protein; MI, meiosis I; NM, nuclear membrane; SKS, SUN–KASH–SPB; SPB, spindle pole body. Introduction
Chionea (Chionea) mirabilis n. sp., a new species of snow fly (Insecta, Diptera, Limoniidae) from Korea

Winter-active insects have attracted the attention of numerous biologists. Since the beginning of the 19th century such research focused on their ecology (activity on snow cover, caves, burrows) and morphology (apterism). Th e most abundant winter active insects belong to the Diptera. Th e snow crane fl ies belonging to the genus Chionea (Diptera, Limoniidae) have an Holarctic distribution with 14 Palaearctic and 18 Nearctic species. Few data about these organisms have been reported from Eastern Asia. Th is region represents a very interesting area, from a biogeographical point of view, to investigate the spread and evolution of this genus. In this paper Chionea (Chionea) mirabilis n. sp. , from South Korea is described and illustrated. Th is species shows two very interesting particularities not present in other species: the apically enlarged tibiae and wings that are longer than in the other described species.
FROM STRUCTURE TO FUNCTION OF RNA BINDING DOMAINS

AbstractR NA binding proteins (RBPs) are involved in each step of RNA metabolism. Most of them are composed of small RNA binding domains (RBDs) that are needed for their recruitment to specific RNA targets. The mode of RNA recognition of these RBDs has been studied by structural biologists for more than 20 years and seems to be highly versatile. In this chapter we review the current structural knowledge about RNA recognition by the four main RBD families, namely RNA recognition motifs (RRMs), zinc fingers, KH domains and double‑stranded RNA binding motifs (dsRBMs) detailing how structural data have brought information essential for a better understanding of RBP functions. Introduction This book focuses on the extreme variety of functions carried by RNA binding proteins (RBPs). The association of RBPs with RNA transcripts begins during transcription. Some of these early‑binding RBPs remain bound to the RNA until they are degraded, whereas others recognize and transiently bind to RNA at later stages for specific processes such as splicing, processing, transport and localization.
The teaching order of using direct laryngoscopy first may improve the learning outcome of endotracheal incubation

Abstract Background: Endotracheal intubation (ETI) is a life-saving procedure taught to medical students. We examined the influence of the order of teaching ETI through direct laryngoscopy (DL) and video laryngoscopy (VL) on learning by measuring the intubation time and learning curve of trainees, in order to explore ways to improve ETI performance. Methods: Twenty trainees were randomly divided into 2 groups. In the DL-first group, trainees used DL to perform ETI 10 times and then used VL 10 times, while the order was reversed in the VL-first group. Intubation time, number of intubation attempts, the Cormack-Lehane (CL) classification, and adverse events were recorded. The primary outcome was the cumulative summation (CUSUM). The CUSUM equation is defined as , where ct is the cumulative sum. Results: ETI was attempted on 400 patients. The difference in the mean times for the first 10 intubations between the 2 groups was not significant (P > .05). Mean intubation time for second series in the DL-first group was significantly shorter than that of the first series (P < .05), while there were no differences between the 2 series in the VL-first group (P > .05). The mean intubation time in the second series of the DL-first group was shorter than for the first series of the VL-first group (P < .05), while the mean intubation time of the first series by the DL-first group did not differ from the second series by the VL-first group (P > .05). Eighteen attempts were required to achieve an 80% intubation success rate for the DL-first group, while more than 20 attempts were required for the trainees in the VL-first group. Conclusion: We consider that teaching trainees DL for tracheal intubation first. Clinical trial number: ChiCTR-OOR-16008364.
Early Phylogenetic Estimate Of The Effective Reproduction Number Of 2019-nCoV

To reconstruct the evolutionary dynamics of the 2019 novel coronavirus, 52 2019−nCOV genomes available on 04 February 2020 at GISAID were analysed. The two models used to estimate the reproduction number (coalescent−based exponential growth and a birth−death skyline method) indicated an estimated mean evolutionary rate of 7.8 x 10−4 subs/site/year (range 1.1x10−4−15x10−4). The estimated R value was 2.6 (range 2.1−5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.
Analysis of early renal injury in COVID-19 and diagnostic value of multi-index combined detection

Objectives The aim of the study was to analyze the incidence of COVID-19 with early renal injury, and to explore the value of multi-index combined detection in diagnosis of early renal injury in COVID-19. Design The study was an observational, descriptive study. Setting This study was carried out in a tertiary hospital in Guangdong, China. Participants 12 patients diagnosed with COVID-19 from January 20, 2020 to February 20, 2020. Primary and secondary outcome measures The primary outcome was to evaluate the incidence of early renal injury in COVID-19. In this study, the estimated glomerular filtration rate (eGFR), endogenous creatinine clearance (Ccr) and urine microalbumin / urinary creatinine ratio (UACR) were calculated to assess the incidence of early renal injury. Secondary outcomes were the diagnostic value of urine microalbumin (UMA), 1-microglobulin (A1M), urine immunoglobulin-G (IGU), urine transferring (TRU) alone and in combination in diagnosis of COVID-19 with early renal injury. Results While all patients had no significant abnormalities in serum creatinine (Scr) and blood urea nitrogen (BUN), the abnormal rates of eGFR, Ccr, and UACR were 66.7%, 41.7%, and 41.7%, respectively. Urinary microprotein detection indicated that the area under curve (AUC) of multi-index combined to diagnose early renal injury in COVID-19 was 0.875, which was higher than UMA (0,813), A1M (0.813), IGU (0.750) and TRU (0.750) alone. Spearman analysis showed that the degree of early renal injury was significantly related to C-reactive protein (CRP) and neutrophil ratio (NER), suggesting that the more severe the infection, the more obvious the early renal injury. Hypokalemia and hyponatremia were common in patients with COVID-19, and there was a correlation with the degree of renal injury. Conclusions Early renal injury was common in patients with COVID-19. Combined detection of UMA, A1M, IGU, and TRU was helpful for the diagnosis of early renal injury in COVID-19.
The timing of one-shot interventions for epidemic control

The apparent early success in China's large-scale intervention to control the COVID-19 epidemic has led to interest in whether other countries can replicate it as well as concerns about a resurgence of the epidemic if or when China relaxes the interventions. In this paper we look at the impact of a single short-term intervention on an epidemic. We see that if an intervention cannot be sustained long-term, it has the greatest impact if it is imposed once infection levels have become large enough that there is an appreciable number of infections present. For minimising the total number infected it should start close to the peak so that there is no rebound once the intervention is stopped, while to minimise the peak prevalence, it should start earlier, allowing two peaks of comparable size rather than one very large peak. In populations with distinct subgroups, synchronized interventions are less effective than targeting the interventions in each sub-population separately. We do not attempt to clearly determine what makes an intervention sustainable or not. We believe that is a policy question. If an intervention is sustainable, it should be kept in place. Our intent is to offer insight into how best to time an intervention whose impact on society is too great to maintain.
Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 Pneumonia

Aim: The new coronavirus pneumonia (COVID-19) outbreaking at the end of 2019 is highly contagious. Crude mortality rate reached 49% in critical patients. Inflammation matters on disease progression. This study analyzed blood inflammation indicators among mild, severe and critical patients, helping to identify severe or critical patients early. Methods: In this cross-sectional study, 100 patients were included and divided to mild, severe or critical groups. Correlation of peripheral blood inflammation-related indicators with disease criticality was analyzed. Cut-off values for critically ill patients were speculated through the ROC curve. Results：Significantly, disease severity were associated with age (R=-0.564, P<0.001), interleukin-2 receptor (IL2R) (R=-0.534, P<0.001), interleukin-6 (IL-6) (R=-0.535, P<0.001), interleukin-8 (IL-8) (R=-0.308, P<0.001), interleukin-10 (IL-10) (R=-0.422, P<0.001), tumor necrosis factor α (TNFα) (R=-0.322, P<0.001), C-reactive protein (CRP) (R=-0.604, P<0.001), ferroprotein (R=-0.508, P<0.001), procalcitonin (R=-0.650, P<0.001), white cell counts (WBC) (R=-0.54, P<0.001), lymphocyte counts (LC) (R=-0.56, P<0.001), neutrophil count (NC) (R=-0.585, P<0.001) and eosinophil counts (EC) (R=-0.299, P=0.01). Conclusion：With following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >2252μg/L, WBC>9.5*10^9/L or NC >7.305*10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented. Inflammation is closely related to severity of COVID-19, and IL-6, TNFα and IL-8 might be promising therapeutic targets.
Stochastic discrete epidemic modeling of COVID-19 transmission in the Province of Shaanxi incorporating public health intervention and case importation

Before the lock-down of Wuhan/Hubei/China, on January 23rd 2020, a large number of individuals infected by COVID-19 moved from the epicenter Wuhan and the Hubei province due to the Spring Festival, resulting in an epidemic in the other provinces including the Shaanxi province. The epidemic scale in Shaanxi was comparatively small and with half of cases being imported from the epicenter. Based on the complete epidemic data including the symptom onset time and transmission chains, we calculate the control reproduction number (1.48-1.69) in Xian. We could also compute the time transition, for each imported or local case, from the latent, to infected, to hospitalized compartment, as well as the effective reproduction number. This calculation enables us to revise our early deterministic transmission model to a stochastic discrete epidemic model with case importation and parameterize it. Our model-based analyses reveal that the newly generated infections decay to zero quickly; the cumulative number of case-driven quarantined individuals via contact tracing stabilize at a manageable level, indicating that the intervention strategies implemented in the Shaanxi province have been effective. Risk analyses, important for the consideration of resumption of work, show that a large second outbreak is expected if the level of case importation remains at the same level as between January 10th and February 4th 2020. However, if the case importation decreases by 30%, 60% and 90%, the second outbreak if happening will be of small-scale assuming contact tracing and quarantine/isolation remain as effective as before. Finally, we consider the effects of intermittent inflow with a Poisson distribution on the likelihood of multiple outbreaks. We believe the developed methodology and stochastic model provide an important model framework for the evaluation of revising travel restriction rules in the consideration of resuming social-economic activities while managing the disease control with potential case importation.
Precautions are Needed for COVID-19 Patients with Coinfection of Common Respiratory Pathogens

Background: With the ongoing outbreak of Coronavirus Disease 2019 (COVID-19), infected patients within and beyond the epidemic area, Wuhan, China, showed different epidemiological and clinical characteristics. There is a paucity of data concerning coinfection with other common respiratory pathogens in COVID-19 patients outside of Wuhan. Methods: We conducted a double-centre study recruiting 68 patients with severe acute respiratory coronavirus 2 (SARS-CoV-2) infection confirmed by nucleic acid testing in Qingdao and Wuhan from January 17 to February 16, 2020. Indirect immunofluorescence was performed to detect the specific IgM antibody against common respiratory pathogens in collected acute phase serum. Results: Of the 68 patients with SARS-CoV-2 infection, 30 (44.12%) were from Qingdao. The median age of Qingdao and Wuhan patients were 50 (IQR: 37-59) and 31 (IQR: 28-38) years, respectively, and the majority of patients were female in Qingdao (60.00%) and Wuhan (55.26%). Among COVID-19 patients in Qingdao, 24 (80.00%) of them had IgM antibodies against at least one respiratory pathogen, whereas only one (2.63%) of the patients in Wuhan had positive results for serum IgM antibody detection (P<0.0001). The most common respiratory pathogens detected in Qingdao COVID-19 patients were influenza virus A (60.00%) and influenza virus B (53.33%), followed by mycoplasma pneumoniae (23.33%) and legionella pneumophila (20.00%). While the pattern for coinfection in patients with community-acquired pneumonia in Qingdao was quite different, with a positive rate of only 20.90%. Interpretation: We reported a large proportion of COVID-19 patients with coinfection of seasonal respiratory pathogens in Qingdao, northeast China, which differed greatly from the patients in Wuhan, central China. Precautions are needed when dealing with COVID-19 patients beyond the epidemic centre who have coinfection with other respiratory pathogens. We highly recommend adding SARS-CoV-2 to routine diagnostic testing in capable hospitals to prevent misdetection of the virus.
A deterministic epidemic model for the emergence of COVID-19 in China

Coronavirus disease (COVID-19) broke out in Wuhan, Hubei province,China, in December 2019 and soon after Chinese health authorities tookunprecedented prevention and control measures to curb the spreading ofthe novel coronavirus-related pneumonia. We develop a mathematicalmodel based on daily updates of reported cases to study the evolutionof the epidemic. With the model, on 95% confidence level, we estimatethe basic reproduction number, R0 = 2.82 ± 0.11, time between March19 and March 21 when the effective reproduction number becoming lessthan one, the epidemic ending after April 2 and the total number ofconfirmed cases approaching 14408 ± 429 on the Chinese mainlandexcluding Hubei province.
Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis

Background and Objective: WHO Director-General declared that the 2019-nCoV outbreak constitutes a Public Health Emergency of International Concern,and the outbreak is still on-going.Chest CT had been a key component of the diagnostic workup for patients with suspected infection. In this retrospective study, we attempt to summarize and analyze the chest CT features of 2019-nCov infections, and to identify the typical features to improved the diagnostic accuracy of new coronavirus pneumonia (NCP). Methods:Chest CT scans and Clinical data of 21 patients confirmed NCP in our hospital were enrolled.These patients were divided into mild and sever group according to clinical manifestations described by the 6th clinical practice guideline of NCP in China. Main clinical and chest CT features were analyzed and identify. Results: Fever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.More significantly higher incidence (85.7%) of shortness of breath in the severe cases. Multiple lesions in both lungs and with incidence of GGO(100%),vascular enlargement (76.5%) and cobblestone/reticular pattern(70.6%) were the major feature.The incidence of consolidation, mixed pattern and vascular enlargement features were up to 100% in the severe group, significantly higher than that of patients in mild group. In addition, the incidence of air-bronchogram, dilated bronchi with thickened wall and fibrosis in the severe group was significantly higher than that in the mild group. Conclusions: Fever and cough are the typical clinical features of NCP patients, and chest CT mainly manifested as multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern.Changes in these main CT features can indicate development of the disease.
Study of the lymphocyte change between COVID-19 and non-COVID-19 pneumonia cases suggesting other factors besides uncontrolled inflammation contributed to multi-organ injury

Background: The corona virus disease 2019 (COVID-19) shows unusually high transmission rate and unique clinical characteristics, with key pathological mechanism remaining unclear. Here, we analysed the laboratory data based on clinical samples from COVID-19 patients, in parallel comparison with non-COVID-19 pneumonia cases, in an attempt to elucidate the key pathological features of COVID-19 during its infection of the human body. Methods: We analysed biochemical indices and lymphocyte subpopulation in COVID-19 patients, and compare these data from non-COVID-19 pneumonia cases. Correlation analysis was performed between leukocyte subgroups count and biochemical indexes in COVID-19 patients. Results: The study enrolled 110 patients, comprising 88 COVID-19 patients and 22 non-COVID-19 pneumonia cases. We observed significant differences, including abnormal biochemical indices (CRP, LDH, AST, eGFR, and sodium ion concentration) and reduced lymphocyte subsets count, between the COVID-19 patients and non-COVID-19-caused pneumonia cases. Correlation analysis indicates that the count for lymphocyte subsets-but not that for neutrophils and monocytes-exhibits a significant negative correlation with biochemical indices relating to organ injury, in the COVID-19 infected patients. Conclusions: The study indicates significantly different clinical features between 2019 novel coronavirus (2019-nCoV)-caused and non-2019-nCoV-caused pneumonia, especially in terms of lymphocytopenia and organ injury. Notably, correlation analysis demonstrates that tissue damage in COVID-19 patients is attributed to virus infection itself rather than uncontrolled inflammatory responses ("cytokine storm"). These findings provide new insights for developing efficient therapeutic strategies against COVID-19 infection.
Estimation of incubation period distribution of COVID-19 using disease onset forward time: a novel cross-sectional and forward follow-up study

This study estimated the incubation distribution of COVID-19 using the theory of renewal process. We have proposed a novel, accurate low-cost method to estimate the incubation-period distribution of COVID-19 by conducting a cross-sectional and forward follow-up study. We identified those presymptomatic individuals at their time of departure from Wuhan and followed them until the development of symptoms. The renewal process was adopted by considering the incubation period as a renewal and the duration between departure and symptoms onset as a forward time. Such a method enhances the accuracy of estimation by reducing recall bias and using the readily available data. The estimated median incubation period was 7.76 days [95% confidence interval (CI): 7.02 to 8.53], and the 90th percentile was 14.28 days (95% CI: 13.64 to 14.90). By including the possibility that a small portion of patients may contract the disease on their way out of Wuhan, the estimated probability that the incubation period is longer than 14 days was between 5 and 10%.