  We extract the ratio of the down (d) and up (u) parton distribution functions
(PDF's) from the ratio of NMC deuteron and proton structure function
F_2(d)/F_2(p), using corrections for nuclear binding effects in the deuteron,
which are extracted from the nuclear dependence of SLAC F_2 data. Significant
corrections to the d quark distribution in standard PDF's are required,
especially at high x. The corrected d/u ratio is in agreement with the QCD
prediction of 0.2 at x=1. The predictions for the recent CDF W asymmetry data
using PDF's with the corrected d/u ratio give much better agreement at large
rapidity. Using the updated d/u ratio and the most recent world average for
alpha_s, we perform a NLO global fit to all DIS data for F_2 and R, and
estimate the size of the higher twist contributions using both a renormalon
model and an empirical model. We find that with the updated value of alpha_s,
the magnitude of the higher twist terms is half the value of previous analysis.
With the inclusion of target mass and higher twist corrections, the standard
NLO PDF's with the updated d/u ratio describe the SLAC F_2 data up to x=1.0.
When the analysis is repeated in NNLO, we find that the additional NNLO
contributions to R account for most of the higher twist effects extracted in
the NLO fit. The analysis in NNLO indicates that the higher twist effects in R,
F_2 and xF_3 (e.g. GLS sum rule) are very small.
