Miracle-dz/UniFAR-FTUs huggingface dataset:
The Anatomic Pattern of Biliary Atresia Identified at Time of Kasai Hepatoportoenterostomy and Early Postoperative Clearance of Jaundice Are Significant Predictors of Transplant-Free Survival

Objective:The goals of this study were to describe the clinical and anatomic features of infants undergoing Kasai portoenterostomy (KPE) for biliary atresia (BA) and to examine associations between these parameters and outcomes. Methods:Infants enrolled in the prospective Childhood Liver Disease Research and Education Network, who underwent KPE were studied. Patients enrolled in a blinded, interventional trial were excluded from survival analysis. Primary endpoints were successful surgical drainage (total bilirubin less than 2 mg/dL within the first 3 months), transplant-free survival (Kaplan-Meier), and time to transplant/death (Cox regression). Results:KPE was performed in 244 infants (54% female; mean age: 65 ± 29 days). Transplant-free survival was 53.7% and 46.7% at 1 and 2 years post-KPE. The risk of transplant/death was significantly lower in the 45.6% of patients who achieved successful bile drainage within 3 months post-KPE (HR: 0.08, P < 0.001). The risk of transplant/death was increased in patients with porta hepatis atresia (Ohi type II and III vs type I; HR: 2.03, P = 0.030), nonpatent common bile duct (Ohi subtype: b, c, and d vs a; HR: 4.31, P = 0.022), BA splenic malformation syndrome (HR: 1.92, P = 0.025), ascites > 20 mL (HR: = 1.90, P = 0.0230), nodular liver appearance compared to firm (HR: = 1.61, P = 0.008), and age at KPE ≥ 75 days (HR: 1.73, P < 0.002). Outcome was not associated with gestational age, gender, race, ethnicity, or extent of porta hepatis dissection. Conclusion:Anatomic pattern of BA, BASM, presence of ascites and nodular liver appearance at KPE, and early postoperative jaundice clearance are significant predictors of transplant-free survival.
Eco-evolutionary factors drive induced plant volatiles: a meta-analysis.

Herbivore-induced plant volatiles (HIPVs) mediate critical ecological functions, but no studies have quantitatively synthesized data published on HIPVs to evaluate broad patterns. We tested three hypotheses that use eco-evolutionary theory to predict volatile induction: feeding guild (chewing arthropods > sap feeders), diet breadth (specialist herbivores > generalists), and selection history (domesticated plants < wild species). To test these hypotheses, we extracted data from 236 experiments that report volatiles produced by herbivore-damaged and undamaged plants. These data were subjected to meta-analysis, including effects on total volatiles and major biochemical classes. Overall, we found that chewers induced more volatiles than sap feeders, for both total volatiles and most volatile classes (e.g. green leaf volatiles, monoterpenes). Although specialist herbivores induced more total volatiles than generalists, this was inconsistent across chemical classes. Contrary to our expectation, domesticated species induced stronger volatile responses than wild species, even when controlling for plant taxonomy. Surprisingly, this is the first quantitative synthesis of published studies on HIPVs. Our analysis provides support for perceptions in the published literature (chewers > sap feeders), while challenging other commonly held notions (wild > crop). Despite the large number of experiments, we identified several gaps in the existing literature that should guide future investigations.
Cloning and sequencing of the gene encoding a 125-kilodalton surface-layer protein from Bacillus sphaericus 2362 and of a related cryptic gene

Using the vector pGEM-4-blue, a 4,251-base-pair DNA fragment containing the gene for the surface (S)-layer protein of Bacillus sphaericus 2362 was cloned into Escherichia coli. Determination of the nucleotide sequence indicated an open reading frame (ORF) coding for a protein of 1,176 amino acids with a molecular size of 125 kilodaltons (kDa). A protein of this size which reacted with antibody to the 122-kDa S-layer protein of B. sphaericus was detected in cells of E. coli containing the recombinant plasmid. Analysis of the deduced amino acid sequence indicated a highly hydrophobic N-terminal region which had the characteristics of a leader peptide. The first amino acid of the N-terminal sequence of the 122-kDa S-layer protein followed the predicted cleavage site of the leader peptide in the 125-kDa protein. A sequence characteristic of promoters expressed during vegetative growth was found within a 177-base-pair region upstream from the ORF coding for the 125-kDa protein. This putative promoter may account for the expression of this gene during the vegetative growth of B. sphaericus and E. coli. The gene for the 125-kDa protein was followed by an inverted repeat characteristic of terminators. Downstream from this gene (11.2 kilobases) was an ORF coding for a putative 80-kDa protein having a high sequence similarity to the 125-kDa protein. Evidence was presented indicating that this gene is cryptic.
Evaluation of Modified Techniques for Immobilization of Wild Ring-Tailed Lemurs (Lemur catta)

Abstract: Wild ring-tailed lemurs (Lemur catta) can be anesthetized with Telazol via blow dart, but improved techniques are needed so that each lemur is reliably induced with a single dart. Medetomidine-butorphanol (MB) is a good supplemental protocol to be administered once the lemurs are captured, but other protocols may provide longer periods of sedation and immobility. One possible way of increasing the efficacy of each dart is to increase the time it is retained in the leg. In this investigation, a “double-sleeve” technique was used to try to increase the time of dart retention. This technique used a standard silicone sleeve on the needle, along with a second sleeve at the needle hub. Induction values were compared between lemurs darted with double-sleeve needles and those induced with needles that each had a single silicone sleeve. Once the lemurs were induced, supplementation with MB (0.04 mg/kg and 0.2 mg/kg) was compared with supplementation with ketamine-medetomidine (KM) (10 mg/kg and 0.04 mg/kg). Twenty-three lemurs were darted with Telazol by using single-sleeve needles, and 24 were darted with double-sleeve needles. The number of darts per lemur and number of escapes were not different between animals darted with a single sleeve compared with a double-sleeve; thus, there were no significant improvements in induction success with the double-sleeve technique. Adequate sedation and muscle relaxation were achieved with both MB and KM; however, lemurs that received MB were more relaxed and needed fewer additional supplements that those that received KM. Single-sleeve dart needles are recommended for Telazol induction of ring-tailed lemurs via blow dart and MB is preferable to KM for supplemental sedation and muscle relaxation.
A web-based referral system for neurosurgery – a solution to our problems?

Introduction. Accurate handover is very important in the running of all modern neurosurgical units. Referrals are notoriously difficult to track and review due to poor quality of written paper-based recorded information for handover (illegibility, incomplete paper trail, repetition of information and loss of patients). We have recently introduced a web-based referral system to three of our referring hospitals. Aim. To review the experience of a tertiary neurosurgical unit in using the UK's first real time online referral system and to discuss its strengths and weaknesses in comparison to the currently used written paper-based referral system. Method. A retrospective analysis of all paper-based referrals made to our unit in March 2009, compared to 14 months' referrals through the web system. Patterns of information recorded in both systems were investigated and advantages and disadvantages of each identified. Results. One hundred ninety-six patients were referred using the online system, 483 using the traditional method. Significant problems of illegibility and missing information were identified with the paper-based referrals. In comparison, 100% documentation was achieved with the online referral system. Only 63% penetrance in the best performing trust was found using the online system, with significant delays in responding to referrals. Conclusion. Traditional written paper-based referrals do not provide an acceptable level of documentation. We present our experience and difficulties implementing a web-based system to address this. Although our data are unable to show improved patient care, we believe the potential benefits of a fully integrated system may offer a solution.
Sox9 and Sox8 Are Required for Basal Lamina Integrity of Testis Cords and for Suppression of FOXL2 During Embryonic Testis Development in Mice1

ABSTRACT The sex-determining gene Sry and its target gene Sox9 initiate the early steps of testis development in mammals. Of the related Sox genes Sox8, Sox9, and Sox10, all expressed during Sertoli cell differentiation, only inactivation of Sox9 before the sex determination stage at Embryonic Day 11.5 (E11.5) causes XY sex reversal, while Sox9 inactivation after this stage has no effect on testis cord differentiation. We have previously shown that both Sox9 and Sox8 are essential for maintaining testicular function in post-E14.0 Sertoli cells. To gain insight into the molecular and cellular processes underlying the abnormal development of Sox9 and Sox8 mutant testes, we performed a detailed developmental study of embryonic and neonatal stages. We observe a progressive disruption of the basal lamina surrounding the testis cords that starts at E17.5 and already at E15.5 reduced expression levels of collagen IV, collagen IXa3 and testatin, structural components of the basal lamina, and the extracellular matrix transcriptional regulator Scleraxis. Lineage tracing reveals that mutant Sertoli cells delaminate from testis cords and are present as isolated cells between remaining cords. Also, Sox10 expression is strongly reduced in the absence of Sox9 and/or Sox8. Finally, we document increasing expression of the ovarian marker FOXL2 in mutant cords starting at E15.5, indicating progressive transdifferentiation of mutant Sertoli cells. This study shows that Sox9 and Sox8 maintain integrity of the basal lamina to prevent testis cord disintegration and that both factors actively suppress the ovarian program during early testis development.
Adsorbed Mass Fluctuations of a Micro/Nanoresonator Surrounded by an Arbitrary Gas Mixture

Micro/nanoresonator mass and frequency fluctuations caused by sorption processes on a resonator surface are investigated. Arbitrary gas mixture is considered, assuming that particle arrivals at the surface are all poissonian in nature, independent from each other, and that sorption dynamics follows the Langmuir isotherm. Power spectral density for mass fluctuations are derived using the analytical Langevin approach. The results of simulations are given for a silicon micro/nanocantilever in the atmosphere of four gases. The presented analysis is useful for calculation of the ultimate performance of MEMS/NEMS sensors and oscillators, as well as for investigation of the possibilities of their parameters optimization by choosing the gas mixture in the cantilever's atmosphere. Another objective is to consider the possibility of identification of gases in the mixture, based on the power spectral density of the adsorbed mass fluctuation
STIM1 Knockdown Reveals That Store-operated Ca2+ Channels Located Close to Sarco/Endoplasmic Ca2+ ATPases (SERCA) Pumps Silently Refill the Endoplasmic Reticulum*

Stromal interaction molecule (STIM) proteins are putative ER Ca2+ sensors that recruit and activate store-operated Ca2+ (SOC) channels at the plasma membrane, a process triggered by the Ca2+ depletion of the endoplasmic reticulum (ER). To test whether STIM1 is required for ER refilling, we used RNA interference and measured Ca2+ signals in the cytosol, the ER, and the mitochondria of HeLa cells. Knockdown of STIM1 (mRNA levels, 73%) reduced SOC entry by 73% when sarco/endoplasmic Ca2+ ATPases (SERCA) were inhibited by thapsigargin but did not prevent Ca2+ stores refilling when cells were stimulated by physiological agonists. Stores could be fully refilled by increasing the external Ca2+ concentration above physiological values, but no cytosolic Ca2+ signals were detected during store refilling even at very high Ca2+ concentrations. [Ca2+]ER measurements revealed that the basal activity of SERCA was not affected in STIM1 knockdown cells and that [Ca2+]ER levels were restored within 2 min in physiological saline following store depletion. Mitochondrial inhibitors reduced ER refilling in wild-type but not in STIM1 knockdown cells, indicating that ER refilling does not require functional mitochondria at low STIM1 levels. Our data show that ER refilling is largely preserved at reduced STIM1 levels, despite a drastic reduction of store-operated Ca2+ entry, because Ca2+ ions are directly transferred from SOC channels to SERCA. These findings are consistent with the formation of microdomains containing not only SOC channels on the plasma membrane and STIM proteins on the ER but also SERCA pumps and mitochondria to refill the ER without perturbing the cytosol.
Testosterone deficiency in the aging male

Treatment for hypogonadism is on the rise, particularly in the aging population. Yet treatment in this population represents a unique challenge to clinicians. The physiology of normal aging is complex and often shares the same, often vague, symptoms of hypogonadism. In older men, a highly prevalent burden of comorbid medical conditions and polypharmacy complicates the differentiation of signs and symptoms of hypogonadism from those of normal aging, yet this differentiation is essential to the diagnosis of hypogonadism. Even in older patients with unequivocally symptomatic hypogonadism, the clinician must navigate the potential benefits and risks of treatment that are not clearly defined in older men. More recently, a greater awareness of the potential risks associated with treatment in older men, particularly in regard to cardiovascular risk and mortality, have been appreciated with recent changes in the US Food and Drug Administration recommendations for use of testosterone in aging men. The aim of this review is to provide a framework for the clinician evaluating testosterone deficiency in older men in order to identify correctly and treat clinically significant hypogonadism in this unique population while minimizing treatment-associated harm.
Tolerability and Safety of HIV Protease Inhibitors in Adults

SummaryAntiretroviral drugs are associated with both short-term and long-term adverse events. Like other HIV drugs, protease inhibitors (PIs) may affect metabolic processes influencing body shape and body tissue composition, appearance, bone integrity, and cardiovascular status. However, numerous confounding variables including age, cigarette smoking, body mass index (BMI), duration of HIV infection, degree of immunodeficiency, concomitant antiretroviral agents, extent of previous treatment, and duration of treatment all blur the relationship between PI use and adverse events. Recent data suggest that the early PIs appear to have greater effects on such surrogate markers of disease risk as insulin resistance and cholesterol and triglyceride levels than the recently developed PIs. These data also suggest that evaluation of PIs as a class should be reconsidered and that it is probably not appropriate to extrapolate safety data obtained from individuals treated with first-generation agents in the era of potent combination antiretroviral therapy to those treated with recently developed PIs. Because PIs remain a critical component of successful antiretroviral therapy, evaluation of potential long-term complications with prolonged PI use is essential, as is delineation of the significant differences in safety profiles among individual PIs.
Characterization with Crossed Immunoelectrophoresis of Some Antigens Differentiating a Virulent Candida albicans from Its Derived, Avirulent Strain

Abstract Antigenic differences between a wild-type virulent Candida albicans 4918 (wt) and its spontaneous avirulent mutant (m-10) were found with crossed immunoelectrophoresis. Yeast cell extracts as well as soluble protein and mannoprotein fractions obtained by affinity chromatography on concanavalin A (Con A) were analyzed. Sera from patients with candidiasis and antisera from rabbits infected with live wt cells and boosted with wt extracts or rabbits immunized with purified wt cell wall preparation were used as counter reactants. Qualitative differences in serum precipitins formed by patients with suspected or culture-proven candidiasis to polysaccharide antigens of wt and m-10 origin were observed. In comparison, except for a spike-formed precipitate detected only with the wt extract, the serum from infected rabbits precipitated the wt and m-10 cell wall polysaccharide antigens about equally. The same type of precipitate was also found with the Con A wt mannoprotein fractions but was again lacking with the m-10 mannoproteins. This precipitate, with extremely slow electromobility in the first dimension, may be related to some special immunodeterminant of the wt mannan molecule. No substantial differences in the precipitation patterns of the Con A wt and m-10 proteins were found when analyzed with patients'sera or rabbit anti-cell sera. However, using these protein fractions with anti-cell wall sera revealed a larger number of precipitates for the wt as opposed to the m-10 strain. The observed antigenic differences between the virulent- and the avirulent-derived strains seem to be mainly associated with cell wall determinants (components) and might be related to the greater adherence and infectivity of the wild strain.
Range of motion training in brace vs. plaster immobilization after anterior cruciate ligament reconstruction: a prospective randomized comparison with a 2‐year follow‐up

The purpose of this prospective and randomized study was to compare rehabilitation with early range of motion (ROM) training vs immobilization following anterior cruciate ligament (ACL) reconstruction. Fifty patients, undergoing an ACL reconstruction with a bone–patellar tendon–bone graft, were postoperatively allocated randomly to either a plaster cast or a brace for 5 weeks. The brace group had ROM exercises from postoperative day 7. The commencement of ROM exercises was postponed 4 weeks for the plaster group compared to the brace group, but progressed subsequently with equal speed. There was no difference between the groups in the ROM of flexion or extension 20 weeks after the ACL reconstruction and later. Twenty‐four months after surgery, the muscle strength deficit in the hamstring muscles (isokinetic measurements; percent difference, injured vs uninjured) was significantly larger in the brace group (mean ± SD: 5.9 ± 7.8%, P < 0.01) than in the plaster group (− 0.9 ± 11.8%, NS) (brace vs plaster group, P < 0.05). Furthermore, there was also a tendency in the brace group to a larger strength deficit in the quadriceps muscle (brace: 11.1 ± 13.2%, P < 0.001; plaster: 3.8 ± 12.9%, NS) (brace vs plaster group, P= 0.07). There was no difference between the groups in the total sagittal knee laxity, as measured with an arthrometer, or in the subjective knee function or activity level (Lysholm score together with the Tegner activity level) between the groups. It is concluded that the postoperative treatment with early range of motion training after ACL reconstruction gave as good ROM, knee stability, subjective knee function and activity level as the treatment with immobilization. It is hypothesized that the larger strength deficit observed after rehabilitation with early range of motion training is secondary to the more intensive training and physical therapist involvement that was demanded in order to achieve full ROM following immobilization.
Characteristic length of the knotting probability revisited

We present a self-avoiding polygon (SAP) model for circular DNA in which the radius of impermeable cylindrical segments corresponds to the screening length of double-stranded DNA surrounded by counter ions. For the model we evaluate the probability for a generated SAP with N segments having a given knot K through simulation. We call it the knotting probability of a knot K with N segments for the SAP model. We show that when N is large the most significant factor in the knotting probability is given by the exponentially decaying part exp(−N/NK), where the estimates of parameter NK are consistent with the same value for all the different knots we investigated. We thus call it the characteristic length of the knotting probability. We give formulae expressing the characteristic length as a function of the cylindrical radius rex, i.e. the screening length of double-stranded DNA.
A 77 GHz SiGe mixer in an embedded wafer level BGA package

We present a fully operational 77 GHz SiGe mixer assembled in a chip-scale embedded wafer level BGA (eWLB) package. This innovative package has a footprint with a standard pad pitch of 0.5 mm and a standard package height of 0.4 mm. The results demonstrate an excellent potential of the eWLB package concept for mm-wave applications. The measured gain of the packaged mixer is in best case only 1 dB smaller than measured on-wafer. Further, we analyze the transition from the printed circuit board (PCB) to the chip in package. We compare the results of our analysis with the measured performance of the packaged mixers. We achieve a good agreement between simulations and measurements. Finally, we discuss the methods for improving the electrical performance of the packages assembled on the PCB.
Comparison of routing protocols performance using wireless mesh network simulation and testbed

Wireless Mesh Network (WMN) has received considerable attention as a means to achieve connectivity in community and commercial networks. Protocols at different stack layers have varying effects both on the energy consumption and the general performance of WMN backbone nodes. Previous studies have shown that, simulations have often been used to obtain protocol performance data, but simulation results are at best an abstraction of the real world network performance. Thus, simulations often provide an unrealistic measure of protocol performance and testbed-based studies are proving more realistic. This paper analyses the performance of AODV and OLSR routing protocols in WMN using both simulation and indoor testbed. Although, the simulation and testbed results aligned with each other for Packet delivery ratio and average throughput, but the magnitude of the difference between the two results is wide. However, the simulation result contradicts that of the testbed for the lifetime. Based on the results of this study, we argue that simulation results only give a rough estimate of the real world network performance. Hence, whenever it is feasible, validating simulation results using a testbed is highly recommended in order to improve our understanding of protocol performance.